AbstractA coupled atmosphere–ocean data assimilation system, the Meteorological Research Institute‐Coupled Data Assimilation System Version 1 (MRI‐CDA1), was developed based on the coupled atmosphere–ocean general circulation model and separate atmosphere and ocean analysis routines operated by the Japan Meteorological Agency (JMA). To implement coupled atmosphere–ocean data assimilation, 6‐hr data assimilation cycles with the coupled model in the outer loop are adopted in atmospheric data assimilation, whereas incremental analysis updates with 10‐day data assimilation cycles are adopted in ocean data assimilation. A coupled data assimilation (reanalysis) experiment (CDA‐Exp) is conducted using MRI‐CDA1 along with an uncoupled reanalysis experiment (UCPL‐Exp) in which the same atmospheric component of the coupled model is forced by prescribed sea surface temperature (SST) similarly to the JMA reanalysis, JRA‐55. Climatological precipitation and variations in precipitation and sea surface air temperature (SAT) are better represented in CDA‐Exp than in JRA‐55, which is brought about by the modification of the atmosphere model physics of the coupled model to better represent climate states. In CDA‐Exp, the SST adjustment to the atmosphere amplifies the lead/lag correlations between subseasonal variations of SST and precipitation. The atmosphere–ocean coupling generates SST variations associated with tropical instability waves, and the SAT field responds to SST variations. The SST–precipitation and SST–SAT relationships on the weather timescale are also recovered in CDA‐Exp, although they are hardly seen in UCPL‐Exp. The coupled model physics generates weather‐timescale SST variations consistent with the atmospheric state, and the atmospheric parameters respond to the SST variations through the coupled model physics. This study suggests that the benefits of coupled data assimilation would be more evident if the ability of MRI‐CDA1 to represent SST variations and its interaction with the atmosphere are improved.