Ecological compensation is an effective means to adjust relationships among stakeholders in order to conserve and/or sustainably use ecosystem services. The current ecological compensation standards (ECS) do not well reflect the differences in ecological, social, and economic development. Thus, we took a typical urbanization area (the Suzhou–Wuxi–Changzhou region) in China as an example, because of its prominent contradiction between rapid socio-economic development and fragile ecosystem. Combined with the ecological, economic, and social conditions, the methods of ecosystem service value (ESV) evaluation, cluster analysis, and scenario analysis were used to propose an optimized spatial zoning method and optimal development scenario. Then, the ECS by different zones were determined by using ESV assessment, cost-benefit analysis, and contingent valuation method. The results showed that (1) the regions were divided into two categories, with a total of four zones: ESV output areas (synergetic development zones (SDZ) and ecological conservation zones (ECZ)) and ESV input areas (ecological degradation zones (EDegZ) and economic development zones (EDevZ)); (2) among five scenarios, the best development mode in the future was the protection and development scenario, which was consistent with the existing planning; and (3) the ECS for the SDZ should be paid about 1.94 billion Yuan/year, the ECZ should be paid about 0.80 billion Yuan/year, the ECS for the EDegZ should pay about 2.20–2.25 million Yuan/year, and the EDevZ should pay about 0.06–7.33 million Yuan/year. By feasibility analysis, the ESV input areas were fully capable of inter-regional compensation, which could promote the effective purchase of ecological services. The developed evaluation framework of ECS in this study can accurately provide a scientific basis for the determination of ecological compensation regulations and policies in the future.