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The Greenhouse Gases Observing Satellite (GOSAT) can help to ascertain the global distribution of carbon dioxide (CO₂) and methane (CH₄), and how the sources and sinks of these gases vary by season, year, and location. However, the data provided by the GOSAT level 2 and 3 products have certain limitations due to their lack of spatial and temporal information; even with the application of the kriging geostatistical method on the level 2 products, the processing algorithms still need further upgrades. In this study, we apply an empirical orthogonal function (EOF)-based method on the GOSAT L3 products (137 images, from January 2010 to May 2021) to estimate the column average of carbon dioxide and methane (XCO₂–XCH₄) within the entire Earth. The reconstructed results are validated against the Total Carbon Column Observing Network (i.e., TCCON), with 31 in situ stations, and GOSAT L4B column-averaged data, using 107 layers. The results show an excellent agreement with the TCCON data and exhibit an R-squared coefficient of 0.95 regarding the CO₂ measurements and 0.86 regarding the CH₄ measurements. Therefore, this methodology can be incorporated into the processing steps used to map global greenhouse gases.