This paper uses a fully coupled general circulation model (CGCM) to study the leading averaged coupled covariance (LACC) method in a strongly coupled data assimilation (SCDA) system. The previous study in a simple coupled climate model has shown that, by calculating the coupled covariance using the leading averaged atmospheric states, the LACC method enhances the signal-to-noise ratio and improves the analysis quality of the slow model component compared to both the traditional weakly coupled data assimilation without cross-component adjustments (WCDA) and the regular SCDA using the simultaneous coupled covariance (SimCC).Here in Part II, the LACC method is tested with a CGCM in a perfect-model framework. By adding the observational adjustments from the low-level atmosphere temperature to the sea surface temperature (SST), the SCDA using LACC significantly reduces the SST error compared to WCDA over the globe; it also improves from the SCDA using SimCC, which performs better than the WCDA only in ...