BACKGROUND : China has achieved zero indigenous malaria case report in 2017. However, along with the increasing of international cooperation development, there is an increasing number of imported malaria cases from Chinese nationals returning from malaria-affected countries. Previous studies have focused on malaria endemic areas in China. There is thus limited information on non-endemic areas in China, especially on the performance of malaria surveillance and response in health facilities. METHODS : A comparative retrospective study was carried out based on routine malaria surveillance data collected from 2013 to 2017. All imported malaria cases reported within the mainland of China were included. Variables used in the comparative analysis between cases in former endemic and former non-endemic areas, included age, gender and occupation, destination of overseas travel, Plasmodium species and patient health outcome. Monthly aggregated data was used to compare seasonal and spatial characteristics. Geographical distribution and spatial-temporal aggregation analyses were conducted. Time to diagnosis and report, method of diagnosis, and level of reporting/diagnosing health facilities were used to assess performance of health facilities. RESULTS : A total of 16 733 malaria cases, out of which 90 were fatal, were recorded in 31 provinces. The majority of cases (96.2%) were reported from former malaria endemic areas while 3.8% were reported from former non-malaria endemic areas. Patients in the age class from 19 to 59 years and males made the highest proportion of cases in both areas. There were significant differences between occupational categories in the two areas (P <  0.001). In former endemic areas, the largest proportion of cases was among outdoor workers (80%). Two peaks (June, January) and three peaks (June, September and January) were found in former endemic and former non-endemic areas, respectively. Time between the onset of symptoms and diagnosis at clinics was significantly different between the two areas at different level of health facilities (P <  0.05). CONCLUSIONS : All the former non-endemic areas are now reporting imported malaria cases. However, the largest proportion of imported cases is still reported from former endemic areas. Health facilities in former endemic areas outperformed those in former non-endemic areas. Information, treatment, and surveillance must be provided for expatriates while capacity building and continuous training must be implemented at health facilities in China.