Global warming and climate change can potentially change not only rice production but also rice nutrient content. To adapt a rice-dependent country’s farming to the impacts of climate change, it is necessary to assess and monitor the potential risk that climate change poses to agriculture. The aim of this study was to clarify the relationship between rice grain protein content (GPC) and meteorological variables through unmanned aerial vehicle remote sensing and meteorological measurements. Furthermore, a method for GPC estimation that combines remote sensing data and meteorological variables was proposed. The conclusions of this study were as follows: (1) The accuracy and robustness of the GPC estimation model were improved by evaluating the nitrogen condition with the green normalized difference vegetation index at the heading stage (GNDVIheading) and evaluating photosynthesis with the average daily solar radiation during the grain-filling stage (SRgrain-filling). GPC estimation considering SRgrain-filling in addition to GNDVIheading was able to estimate the observed GPC under the different conditions. (2) Increased temperature from the transplantation date to the heading stage can affect increased GPC when extreme temperature does not cause the heat stress.