Background: New Rural Cooperative Medical Scheme (NRCMS) was developed to improve the health security for rural residents. This study aimed to assess the trend of disparity between coastland and inland in medical expenditure burden for rural inpatients with malignant tumor from 2007 to 2016 under the effect of NRCMS. Methods: The data from medical records of 1,306,895 patients with malignant tumor who had NRCMS in 2932 hospitals was collected. The relative differences [95% confidence intervals (CIs)] between coastland and inland in four medical expense indicators were calculated using generalized linear models to assess the trend of disparity over time. Results: In total, there were 769,484 (58.88%) coastland patients and 537,411 (41.12%) inland patients. Male and patients aged older than 44 years accounted for 56.87 and 80% of 1,306,895 patients, respectively. After adjusting for gender, age, tumor site and hospital level, coastland patients had higher hospitalization expenses which were all medical expenses incurred during the hospitalization, lower reimbursement ratio and ratio of out-of-pocket expenses to disposable income than inland patients in most years. The surgery expenses of coastland patients were lower than those of inland patients in 2016. The relative differences (95% CIs) between coastland and inland in medical expense indicators were moving closer to 1.0 from 2007 to 2010 among patients without surgery, implying that the disparity between two areas significantly narrowed. The range of change was similar between two areas from 2011 to 2016 whether among patients without or with surgery, implying that the disparity did not significantly change. The disparity between coastland and inland depended on the household income situation. For low-income patients, the differences between two areas in medical expense indicators were not statistically significance in most cases and the disparity between two areas did not significantly change over time.