The near-term climate prediction system (DecPreS) is built on the initialization of the ocean state, which can be regarded as a full-coupled system with “adjusted” air-sea interactions. The relationship between stratocumulus and Sea Surface Temperature (SST ) is an essential part of air-sea interactions. In this study, we investigated such a relationship in DecPreS of the Institute of Atmospheric Physics, in which the merge of the Ensemble Optimal Interpolation (EnOI) and Incremental Analysis Update (IAU) scheme was employed. EnOI-IAU generally reproduces the spatial pattern of SST and low-clouds. However, the simulated cloud fraction/liquid water path are underestimated while the SST is overestimated in stratocumulus regimes, especially in the subtropical East Pacific and South Ocean. It is partly because the unrealistic air-sea interaction dominates these regions that the underestimated stratocumulus allows more input of incoming shortwave flux (20 W/m2). The deficient stratocumulus is highly related to the unrealistic vertical structure of Atmospheric Boundary Layer (ABL), in which the moisture, temperature and vertical heat transports concentrate at the surface layer. Our results imply that stratocumulus and ABL be important in DecPreS. Clarifying the importance of ABL and stratocumulus will provide a possible way to improve the DecPreS.