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As semi‐enclosed and shallow seas, the Bohai and Yellow Seas (hereafter, BYS) marine ecosystems are more easily affected by natural and anthropogenic climate changes than those in the open oceans. An accurate assessment of sea surface temperature (SST) change is crucial for the near‐shore water environment. In this work, new high‐quality monthly mean SST time series from 11 in situ coastal hydrological stations at BYS for the period of 1960–2012 have been generated. Monthly mean SST time series were initially subjected to penalized maximal t (PMT) test, using homogeneous monthly mean surface air temperature (SAT) series as references. Homogenized monthly mean SST series were obtained by adjusting all significant change points which have been supported by historic metadata. Our study shows that there are 29 significant change points in these 11 SST series. The majority of them are caused by instrument changes and station relocations—both account for about 51.7 and 31%, respectively. Then, homogeneous SST series are used to assess the long‐term trends. As the regional average, the annual mean homogeneous SST series shows a rapid warming trend, with the rate of 0.21°C/decade. Compared to the homogeneous SST series, the original SST series underestimate the long‐term trend (only 0.13°C/decade), indicating the artificial change points usually result in a warm‐bias in the early period measurements. Seasonally, the most significant warming occurs in boreal winter during the period analysed. The relationships of the significant warming in boreal winter and atmospheric circulation modes have also been investigated. Results reflect the remarkable and direct influence of the East Asian Trough (EAT) on SST along the coastal BYS. [ABSTRACT FROM AUTHOR]