Objective To assess the case-based malaria surveillance and response during the period of COVID-19 outbreak in China, in order to provide reference for malaria elimination under the COVID-19 pandemic. Methods Information of malaria cases reported during the four months pre- and post-COVID-19 outbreak (December 1, 2019—March 31, 2020) and in the same time period of past two years in China (excluding Hong Kong, Macau and Taiwan regions) was obtained from the Parasitic Disease Control Information Management System. Cross-sectional survey and comparison were conducted for malaria surveillance and response data in 3 four-month time periods (December 1, 2019 to January 22, 2020; January 23 to March 17, 2020; and March 18—31, 2020). The number of malaria cases including deaths, the median and average time interval from disease onset to the first visit, the median and average of time interval from the first visit to the confirmed diagnosis, the completion status of the “1-3-7” task and the source of infections in each period were analyzed and compared to the same times in the past two years. Results From December 1, 2019 to March 31, 2020, a total of 750 malaria cases, which were all imported cases, were reported in China, decreased by 9.2% from that reported during December 2018 and March 2019 (826 cases) and by 13.1% from that reported during December 2017 to March 2018 (863 cases). The decrease mainly occurred in February and March in 2020; there were no statistical differences in the time interval from onset to first visit (median 1 day, mean 2.0 days), time interval from first visit to confirmed diagnosis (median 1 day, mean 1.8 days), case reporting rate within 1 day (100%), case epidemiological investigation rate within 3 days (98.4%), epidemic site disposal rate within 7 days (100%) between the time period of COVID-19 outbreak and the same time in the past year (December 2018 to March 2019). In addition, no statistical difference (P > 0.05) was found in the time intervals from onset to first visit among the first period [median 1 d, average (1.9 ± 0.2) d], the second period [median 1 d, average (2.1 ± 0.3) d] and the third period [median 1 d, mean (1.5 ± 0.3) d], while the time interval from the first visit to the confirmed diagnosis was statistically different (P < 0.05) among the first period[median 0 d, average (1.5 ± 0.2) d], the second period [median 1 d, mean (2.3 ± 0.3) d] and the third period [median 0.5 d, average (1.5 ± 0.4) d], where the time interval in the second period was longer than that in the first period (P < 0.01). Conclusion China’s core measures to eliminate malaria have been carried out as planned, although the timely malaria diagnosis was slightly affected in the second time period (January 23 to March 17, 2020).