Objective To explore the impact of diagnosis-related group (DRG) payment method reform under total amount control on neurology and neurosurgery departments. Methods The DRG grouping data of the Department of Neurology and the Department of Neurosurgery of Panzhihua Central Hospital from January 2018 to December 2020 were collected, and the mature DRG evaluation indexes in China were selected. Using the interrupt time series analysis method, the DRG-related indexes of the two departments before and after the introduction of the performance appraisal plan in July 2019 were compared, to evaluate the intervention effects on the two departments. Results Both neurology and neurosurgery departments showed a slow downward trend in the overall medical service capacity under the DRG payment. The efficiency of medical services showed a slow upward trend and the consumption of medical expenses showed a slow downward trend in the Department of Neurology, while the efficiency of medical services showed a slow downward trend and the consumption of medical expenses showed a slow upward trend in the Department of Neurosurgery. According to the results of interrupt time series analysis, in the Department of Neurosurgery, the total weight showed a significant downward trend before intervention (β1=−5.526, P=0.003), and the downward trend became sluggish after intervention, with a statistically significant slope difference before and after intervention (β3=4.546, P=0.047); the case-mix index showed a downward trend before intervention (β1=−0.050, P<0.001), and no obvious trend after intervention, with a statistically significant slope difference before and after intervention (β3=0.052, P=0.001); the cost consumption index showed no obvious downward trend before intervention (β1=−0.006, P=0.258), and an upward trend after intervention, with a statistically significant slope difference before and after intervention (β3=0.027, P=0.032). The impact of this assessment plan on the Department of Neurology was not statistically significant (P>0.05), needing further observation. Conclusions The reform of DRG payment method under total amount control has different effects on the evaluation indicators of clinical departments of different natures. It is recommended to implement classified management and assessment for clinical departments of different natures.