This paper introduces a novel ensemble adjustment Kalman filter (EAKF) that integrates a machine-learning approach. The approach employs nonlinear variable relationships established by a deep neural network (DNN) during the analysis stage of the EAKF. This process nonlinearly projects observation increments into the state variable space. The newly developed DNN-EAKF algorithm can be applied to coupled data assimilation using coupled ocean-atmosphere models. It enhances cross-component updates in strongly coupled data assimilation (SCDA) by diminishing errors in estimating cross-component error covariance arising from insufficient ensemble members, thereby improving the SCDA analysis. This paper employs a conceptual model to conduct twin experiments, validating the DNN-EAKF’s capability to utilize cross-component observation information in SCDA effectively. The approach is anticipated to offer insights for future methodological integrations of machine learning and data assimilation and provide methods for SCDA applications in coupled general circulation models.