This study aims to ascertain the long-term epidemic trends of malaria and evaluates the probability of achieving the eradication goal by 2020 in China. Data on malaria incidence and deaths were extracted from the China Information System for Disease Control and Prevention. The epidemic trends by sex, age and spatial distribution and predictions of malaria were estimated by using Joinpoint and Poisson regressions. From 1950 to 2016, 227 668 374 malaria cases were reported in China, with an annualised average incidence of 337.02 (336.98–337.07, 95% confidence interval (CI)) per 100 000 population. The incidence decreased with an average annual per cent change (AAPC) of −11.4% (−16.6 to −6.0). There were 36 085 malaria deaths, with an annualised average mortality of 0.534 (0.529–0.540) per 1 000 000 population. The mortality decreased with an AAPC of −8.7% (−13.7 to −3.4). The predicted number of malaria cases and deaths for 2020 is 2 562 and 10, respectively, and zero for indigenous cases. The disease burden of malaria dramatically decreased in China. Though, the goal of malaria elimination is realistic by 2020 in China, routine clinical and entomological surveillance should be continually conducted, especially for the cross-border areas and imported malaria cases.