Abstract The North Pacific is divided into different regions based on ocean currents and sea surface temperature (SST) distribution. Data assimilation is a useful tool for generating accurate ocean estimates because of the limited availability of observational data. This study compared the performances of two data assimilation methods, ensemble optimal interpolation (EnOI) and ensemble Kalman filter (EnKF), in various North Pacific subregions using an ocean model configured with the Regional Ocean Modeling System (ROMS). Both methods assimilated spaceborne SST observations, and the simulation results varied by subregion. The study found that EnKF and EnOI methods performed better than the control model in all regions when compared against satellite SST. EnOI reproduced SST as well as EnKF and required fewer computational resources. However, EnOI performed worse than the control model at sea surface height (SSH) in the equatorial region, while EnKF’s performance improved. This was due to the crushed mean state in the EnOI, which used long-term historical data as an ensemble member. El Niño–Southern Oscillation at the equator drove substantial interannual variability that crushed the ensemble mean of SSH in the EnOI. It is crucial to use a suitable assimilation method for the target area, considering the regional properties of ocean variables. Otherwise, the performance of the assimilated model may be even worse than that of the control model. While EnKF is better suited for regions with high variability in ocean variables, EnOI requires fewer computational resources. Thus, it is crucial to use a suitable assimilation method for accurately predicting and understanding the dynamics of the North Pacific.