Biodiversity has long been the main objectives in conservation planning while protecting ecosystem services are rarely concerned with. Protecting ecosystem services are gradually recognized by researchers to be included in conservation planning as its significant benefits to human beings. Currently, the most commonly used protecting strategies only focused on high-value areas so that not all the valuable areas would be protected. Furthermore, there are correlation of trade-off and synergy between ecosystem services, aiming at protecting one ecosystem service may have to sacrifice the conservation effectiveness for others. To ensure all the ecosystem services are adequately protected, spatial explicit relations between all the paired ecosystem services were identified via the calculation of Local Moran’s I, a local scale relationship between ecosystem services were defined and they were classified into 5 kinds of cluster. To alleviate the conflict solutions for multiple ecosystem services goals, we used methodology of Systematic Conservation Planning to identify the priority areas for ecosystem service protection, which act the plan with principles of representativeness, complementarity and persistence. By setting scenarios of optimizing each and all the ecosystem services at the target level from 10% to 90%, we found that positive correlation between each of the 4 ecosystem services occupied large areas in the Yangtze River Basin and all the high-value areas were not congruence in spatial distributions. The optimal conservation spatial pattern showed that the priority areas were quite different when the target level was low. Our results implicated that an integrated conservation planning of achieving objectives of all the ecosystem services is more efficient than superposing multiple planning time after time.