Objective To audit and assess the credibility of malaria case information reported by National Information Management System for Malaria in 2017 and identify the problems and gaps in the malaria case report network, and provide the corresponding suggestions for improving the system accordingly. Methods The malaria cases reported by National Information Management System for Malaria from 24 malaria-endemic provinces and the case information were audited and re-assessed by National Technical Committee for Malaria Elimination. The audit results for the report credibility of malaria cases in different provinces, different seasons and different regions, and their influences were statistically analyzed using descriptive statistics, chi-square tests and trend tests. Results A total of 2 651 malaria cases reported in 24 malaria endemic provinces (municipalities, autonomous region) in 2017 and the case information were audited and re-assessed by the committee experts, only 58.17% (1 542/2 651) of which were qualified through the preliminary assessment. The preliminarily assessed qualified rate for each case of quarter were 58.18% (377/648), 61.73% (450/729), 48.85% (360/737) and 66.11% (355/537), respectively, with no significant linear trend(P > 0.01). The qualified rate of preliminary assessment for cases collected from Eastern, Central and Western endemic regions were 55.96% (856/1 529), 60.35% (312/517) and 61.82% (374/605), respectively, without significant difference among them. The three provinces with the lowest assessment qualification rate were Hubei (36.00%, 36/100), Guizhou (37.50%, 9/24) and Hebei (40.68%, 24/59). The main reasons for the unqualified case report included the lack of provincial-level re-assessment (29.23%), insufficient evidence for case diagnosis (5.17%), incomplete case information (5.28%) and irregular antimalarial medication(2.15%). After being re-assessed through adding and collecting more information, the qualified rate of reported malaria cases increased to 92.49% (2 452/2 651) and the above mentioned unqualified reasons dropped to 3.06% (lack of provincial-level re-assessment), 2.04% (insufficient evidence), 1.36% (incomplete information) and 1.06% (irregular treatment), with statistical significance compared to the preliminary assessment results (P < 0.01). The re-assessment also increased the qualified rate of malaria cases reported in each quarter with 89.81% (582/648) for the 1st quarter, 91.08% (664/729) for the 2nd quarter, 93.08% (686/737) for the 3rd quarter and 96.83% (520/537) for the 4th quarter with linear trend (P < 0.01). However, there was no statistically significant difference in the unqualified rate of re-assessment in different regions (P > 0.01). The re-assessed qualified rate for cases reported in the eastern, central and western regions increased to 93.07% (1 423/1 529), 90.72% (469/517) and 92.56% (560/605) respectively, with no statistically significant difference among the different regions (P > 0.01). However, the rate of irregular antimalarial medication in western region (2.51%, 13/605) was higher than that in the central (1.93%, 10/517) and eastern (0.33%, 5/1 529) regions with statistical significance (P < 0.01), whereas the other unqualified reasons had no statistical difference among different regions (P > 0.01). The three provinces with the lowest qualified rate of malaria case report after being re-assessed were Guizhou (75.00%, 18/24), Henan (82.49%, 76/177) and Gansu (15/18). Conclusion Re-assessment of reported national malaria cases and case information have improved the qualification and accuracy of malaria cases reported by National Information Management System for Malaria. The main reason for the inaccuracy is the irregularities during the case information report.