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The chlorophyll-a concentration (CHL) data observed with the ocean color sensors have been widely used in the various studies related to phytoplankton. However, irregularly distributed missing data induced by clouds, a unique nature of optics, can cause large uncertainty, and a solution to this missing issue has been continuously demanded until now. We investigated the applicability of the data interpolating empirical orthogonal function and evaluated the reconstruction results in the southwestern East Sea. A total of 311 decomposed modes were used, showing a coefficient of determination of about 0.86 and a root mean square error of 0.37 mg m−3, compared to the truth data. Overall, it was confirmed that the observed CHL was overestimated compared to the reconstructed CHL when the spatio-temporal average was taken.