Objective To analyze the current status of primary surveillance and response system in Fujian Province after malaria elimination, and to provide the scientific basis for the formulation of malaria control and prevention measures. Methods In October 2020, a retrospective survey was carried out on the malaria control and prevention capability in 85 counties (cities and districts) during 2016—2020 in Fujian Province. The survey content included the funding for control, number of technical personnel, medicine back store, detection equipments, designated hospitals, clinical cases monitoring, transmission vector surveillance, and personnel training, combining with the annual malaria control reports in in post-elimination years, to analyze the current status of primary surveillance response system during the malaria post-elimination phase in the province based on the risk ranking of imported cases vs retransmission. SPSS 17.0 software was used for statistical analysis. The measurement data were analyzed using t-test or Wilcoxon rank sum test based on the homogeneity of variance, and the counting data were analyzed using chi-square test. Results A total of 92 280 blood samples were tested in the province from 2016 to 2020, among 505 were positive (0.55%), defined as imported cases. The reported cases first visited primary medical institutions accounted for 23.37%（118/505）, which increased year by year, with statistical significance (χ² = 16.49, P < 0.05). But the initial diagnosis rate was 27.97% (33/118), which did not increase with the number of patients (χ² = 2.50, P > 0.05). A total of 94.12% (80/85) of primary centers for Disease Control and Prevention had funding for malaria control and elimination in the previous three years (2018—2020), with an average of 9 700 yuan per county per year. The average annual funding in counties with higher risk of re-establishment of transmission by Plasmodium vivax was higher (13 500 yuan) than the counties with the potential risk (8 800 yuan). The difference was statistically significant (t = 2.16, P < 0.05). There were 20 primary CDCs (23.53%) without the capacity to detect malaria, which were due to the lack of microscopes or professionals, and 80% of them (16/20) had imported malaria cases in their service areas during the past three years. The percentage of CDCs with antimalarial drugs and rapid diagnostic test (RDT) in primary CDCs were 4.71% (4/85) and 8.24% (7/85), respectively. The percentage of CDCs with RDT in storage in counties with the risk of re-establishment of P. vivax transmission (4/17) were higher than those in counties with potential risk (4.41%, 3/68). The difference was statistically significant (χ² = 4.29, P < 0.05). From 2016 to 2020, a total of 12 040 people were trained in 85 counties of the province. The number of trainings for control and prevention personnel and laboratory personnel showed a downward trend (from 1 509 and 656 in 2016 to 819 and 348 in 2020), while the number of training for clinicians showed an increase trend (from 404 in 2016 to 887 in 2020). From 2018 to 2020, at least one training was organized by 85.88% (73/85) of the counties, but training for village and individual doctors was only organized by 3.53% (3/85) and 2.35% (2/85) of the counties. In three years, the Anopheles mosquito population and density monitoring which were carried out by 29 primary CDCs (34.12%) and 20 CDCs (23.53%). And a total of 8 148 Anopheles were captured, all of which were An. sinensis, but no An. anthropophagus or An. minimus. During the population monitoring by lamp trap, 1.57 An. sinensis per lamp per night were captured in counties with the risk of re-establishment of transmission by P. vivax, which was lower than that in counties with potential risk (2.16 per lamp per night) (χ² = 5.72, P < 0.05). Conclusion After the elimination of malaria in Fujian Province, the capacity of malaria diagnosis and surveillance of primary medical settings is weakening. It is imperative to optimize the surveillance scheme based on the risk ranking, provide stable funding and personnel training to enhance the primary surveillance-response capacity for consolidating the accomplishments of malaria elimination.