Objective To understand the situation of child health services and clinics in county-level maternal and child health (MCH) institutions and provide scientific basis to standardize such clinical services. Methods Multi-stage stratified sampling method was used to investigate the situation of child health clinics of county-level MCH institutions in 2012.The differences and influencing factors of such clinical services among different regions and levels were analyzed. Results The results showed that the rates of setting child health clinics were about 50% in 232 county-level MCH institutions.Not statistically significant difference was observed of the rates of setting outpatients in MCH institutions between county level and district level (P>0.05).The differences of the rate of setting hearing care clinic among eastern, central and western regions were statistically significant (P<0.05).The number of child health clinics was related with the number of staff members and housing area of institutions and child health clinics. Conclusions The situation of child health clinical services at county-level MCH institutions in China is not optimistic for a low setting rate of child health clinic and existing regional differences at various degrees.Thus, it is important to increase the investment on the number of staff and child care clinic facilities.