Background: China launched a new round of National Malaria Eradication Program (NMEP) in 2010 that sets the goal to eliminate malaria by 2020, while it has been challenged by the large-scale frequent population migration. To assess the influence of geographic mobility of population on the epidemiology of malaria, we conducted a comprehensive study about the care-seeking behavior among malaria patients. Methods: The malaria cases were identified within a national database from the National Health Commission of the People’s Republic of China. All health institutions and facilities reported malaria patient records during the period from January 2014 to December 2016. Overall 1633 malaria patients were selected in six provinces located in eastern, central and western China that saw most severe malaria epidemic using stratified sampling. Descriptive statistical analysis was used to investigate the distribution of malaria patients in various medical institutions, and the chi-square test was used to compare the cross-regional visit rates of different types of hospitals. Colored maps were drawn to visualize the spatial distribution of hospitals and spatial flow of malaria patients by using the ArcGIS software. Results: The proportions of malaria patients who sought medical care in general hospitals, township hospitals, and professional public health institutions were 81.7%, 14.7% and 3.6%, respectively. For those who visited hospitals, the percentages who chose provincial, prefecture-level and county-level hospitals for malaria treatment were 17.4%, 60.5% and 22.1%, correspondingly; the proportions of malaria patients who sought medical care in tertiary hospitals, secondary hospitals, and primary hospitals were 59.8%, 39.9% and 0.3%, respectively. Moreover, the proportions of inter-provincial, inter-city and inter-county patients were 3.9%, 82.4% and 80.2%, respectively. In addition, we also found that the percentage of malaria patients who sought treatment in designated hospitals was high. Conclusion: With the implementation of National Malaria Control Program (NMCP), malaria patients tended to seek medical care in designate tertiary hospitals, and slightly more than half of patients could be treated in health institutions and facilities in prefectural area. In the post-stage of malaria elimination, it is necessary to establish prompt response grassroots hospitals to refer malaria patients to designated malaria treatment hospitals.