An ensemble-based assimilation method is proposed for correcting the subsurface temperature field whennudging the sea surface temperature (SST) observations into the Max Planck Institute (MPI) climate model, ECHAM5/MPI-OM. This method can project SST directly to subsurface according to model ensemble-based correlations between SST and subsurface temperature. Results from a 50 year (1960–2009) assimilation experiment show the method can improve the subsurface temperature field up to 300 m compared to the quality-controlled subsurface ocean temperature objective analyses (EN4), through reducing the biases of the thermal states, improving the thermocline structure, and reducing the root mean square (RMS) errors. Moreover, as most of the improvements concentrate over the upper 100 m, the ocean heat content in the upper 100 m (OHT_100 m) is further adopted as a property to validate the performance of the ensemble-based correction method. The results show that RMS errors of the global OHT_100 m convergent to one value after several times iteration, indicating this method can represent the relationship between SST and subsurface temperature fields well, and then improve the accuracy of the simulation in the subsurface temperature of the climate model.