The development and application of a regional ocean data assimilation system are among the aims of the Global Ocean Data Assimilation Experiment. The ocean data assimilation system in the regions including the Indian and West Pacific oceans is an endeavor motivated by this goal. In this study, we describe the system in detail. Moreover, the reanalysis in the joint area of Asia, the Indian Ocean, and the western Pacific Ocean(hereafter AIPOcean) constructed using multi-year model integration with data assimilation is used to test the performance of this system. The ocean model is an eddy-resolving,hybrid coordinate ocean model. Various types of observations including in-situ temperature and salinity profiles(mechanical bathythermograph, expendable bathythermograph, Array for Real-time Geostrophic Oceanography, Tropical Atmosphere Ocean Array, conductivity–temperature–depth, station data), remotely-sensed sea surface temperature, and altimetry sea level anomalies, are assimilated into the reanalysis via the ensemble optimal interpolation method. An ensemble of model states sampled from a long-term integration is allowed to change with season, rather than remaining stationary. The estimated background error covariance matrix may reasonably reflect the seasonality and anisotropy. We evaluate the performance of AIPOcean during the period 1993–2006 by comparisons with independent observations, and some reanalysis products. We show that AIPOcean reduces the errors of subsurface temperature and salinity, and reproduces mesoscale eddies. In contrast to ECCO and SODA products, AIPOcean captures the interannual variability and linear trend of sea level anomalies very well. AIPOcean also shows a good consistency with tide gauges. The development and application of a regional ocean data assimilation system are among the aims of the Global Ocean Data Assimilation Experiment. The ocean data assimilation system in the regions including the Indian and West Pacific oceans is an endeavor motivated by this goal. In this study, we describe the system in detail. Moreover, the reanalysis in the joint area of ​​Asia, the Indian Ocean, and the western Pacific Ocean (hereafter AIPOcean) constructed using multi-year model integration with data assimilation is used to test the performance of this system The types of observations include in-situ temperature and salinity profiles (mechanical bathythermograph, expendable bathythermograph, Array for Real-time Geostrophic Oceanography, Tropical Atmosphere Ocean Array, conductivity-temperature -depth, station data), remotely-sensed sea surface temperature, and altimetry sea level anomalies, are assimilated int o the reanalysis via the ensemble optimal interpolation method. An ensemble of model states sampled from a long-term integration is allowed to change with season, rather than remaining stationary. The estimated background error covariance matrix may reasonably reflect the seasonality and anisotropy. We evaluate the performance of AIPOcean during the period 1993-2006 by comparisons with independent observations, and some reanalysis products. We show that AIPOcean reduces the errors of subsurface temperature and salinity, and reproduces mesoscale eddies. In contrast to ECCO and SODA products, AIPO ce captures the interannual variability and linear trend of sea level anomalies very well. AIPOcean also shows a good consistency with tide gauges.