This study focused on the total precipitable water (TPW) products of Advanced Microwave Scanning Radiometer 2 (AMSR2) onboard the Global Change Observation Mission—Water (GCOM-W). The GCOM-W satellite has been flying in the Afternoon Constellation (A-train) orbit to synergize with other A-train satellites, such as Aqua. In this study, we compared two datasets of AMSR2 TPW from July 2012 to December 2020, independently produced by the Japan Aerospace Exploration Agency (JAXA) and Remote Sensing Systems (RSS). No significant differences were observed in the TPW anomaly trends between the two datasets. However, significant differences were observed in the absolute values of TPW in the northwest Pacific and northwest Atlantic Oceans during the boreal summer season. We investigated the meteorological conditions that caused these differences using reanalysis, in situ observation data, and visible and infrared data from the MODerate resolution Imaging Spectroradiometer (MODIS) on the Aqua. The results indicated that the lower atmosphere had an inversion layer with relative humidity close to 100 %, and very-low-altitude clouds (i.e., fog) were often distributed in the areas where the TPW differences between the JAXA and RSS are significant. The temperature profiles represented in the JAXA and RSS algorithms were approximated by a simple model. The influence of the inversion layer and fog on the JAXA and RSS TPW algorithms was also investigated using a radiative transfer model. Sensitivity experiments suggested that the inversion layer was associated with the underestimated TPW for the JAXA algorithm, whereas it was associated with the overestimated TPW for the RSS algorithm.