The East China Shelf Seas, comprising the Bohai Sea, the Yellow Sea, and the shelf region of East China Sea, play significant roles among the shelf seas of the Western North Pacific Ocean. The projection of sea surface temperature (SST) changes in these regions is a hot research topic in marine science. However, this is a very difficult task due to the lack of available long-term projection data. Recently, with the high development of simulation technology based on numerical models, the model intercomparison projects, e.g., Phase 5 of the Climate Model Intercomparison Project (CMIP5), have become important ways of understanding climate changes. CMIP5 provides multiple models that can be used to estimate SST changes by 2100 under different representative concentration pathways (RCPs). This paper developed a CMIP5-based SST investigation framework for the projection of decadal and seasonal variation of SST in East China Shelf Seas by 2100. Since the simulation results of CMIP5 models may have degrees of errors, this paper uses hydrological observation data from World Ocean Atlas 2018 (WOA18) for model validation and correction. This paper selects seven representative ones including ACCESS1.3, CCSM4, FIO-ESM, CESM1-CAM5, CMCC-CMS, NorESM1-ME, and Max Planck Institute Earth System Model of medium resolution (MPI-ESM-MR). The decadal and seasonal SST changes in the next 100 years (2030, 2060, 2090) are investigated by comparing with the present analysis in 2010. The experimental results demonstrate that SST will increase significantly by 2100: the decadal SST will increase by about 1.55 °C, while the seasonal SST will increase by 1.03–1.95 °C.