Objective To explore the effect of separate management of income and expenditure (SMIE) on standard community healthcare services. Methods Health management records of 137 community health service ( CHS) institutions in Beijing during 2006 and 2009 were retrospectively analyzed. Paired t test was used to compare annual healthcare services at urban and rural areas before or after SMIE was adopted. Results The standard community healthcare services was reduced from 1 081 965. 53 to 971 793. 98 at urban areas and from 157 492. 23 to 149 305. 25 at rural areas (P >0. 05). Urban healthcare center-based standard services was decreased from 59. 94% to 52. 14% (P < 0. 05 ); while out-hospital services were increased from 13. 50% to 18. 88% (P<0. 05). In urban areas,standard services for women healthcare, chronic disease profiling, health education and information management were significantly increased (I <0. 05). However,Temporary observation and endemic disease prevention and treatment were the main job of rural healthcare. Conclusions SMIE in CHS institutions could accommodate to the need of health management, supporting policies should be further improved.