Background: Hospital adherence to evidence-based stroke care is variable and changes over time. We take full account of these variations and determined indicators which could reduce adverse outcomes and narrow inter-hospital variation in stroke patients under the current protocol of clinical treatment for stroke. Methods: We analyzed data from 123259 patients diagnosed with acute ischemic stroke (AIS) who were treated at 109 large tertiary hospitals from January 2011 to May 2017. Hospitals were divided into subgroups according to the time trend of hospital process composite performance (HPCP, that were calculated by the method of opportunity-based score on patient-level) estimated by the Group Based Model. We analyzed the influence of hospital subgroups on the patient outcomes using a multi-level model and explored the quality indicators (QIs) that led to variation. Results: The HPCP trends for stroke indicators of 109 hospitals over 7 years were divided into two groups (Group 1, low-HPCP; Group 2, high-HPCP). Patients in Group 2 tended to have a higher rate of independence (modified Rankin Scale≤2). The multi-level model showed that there was a statistically significant difference in the utilization rate between the two groups, which mainly focused on the emergency examination and function evaluation indicators. Conclusions: Variation in the quality of stroke care exists across hospitals. We found that QIs related to emergency examination and functional assessment were the main factors in different trends of stroke HPCP over time and identifying hospital care differences, suggesting that quality improvement in stroke care could prioritize these QIs.