Bell pepper quality is typically maintained by storage at low temperatures. However, the environment for bell pepper storage during practical postharvest handling still needs to be optimized. Therefore, in this study, an investigation of ripening behavior and related molecular changes of bell peppers stored at various temperatures for 28 days was conducted. Bell pepper fruits were harvested at the mature green stage and held in unsealed polypropylene pouches at 10, 20, or 30 ℃ in the dark. The pericarp color value of the bell peppers confirmed the ripening initiation after 28 days of storage at higher temperatures. An earlier color change was observed on the opposite end of the fruit from the calyx. A gene expression profile plot obtained by RNA-Seq data using microarray data analysis software clearly showed the effects of storage temperature on the gene expression profile. A principal component analysis using two components showed a clear difference among treatments, (storage temperatures). The effects of fruit section, (top, middle, or bottom) on gene expression were minor compared with those of storage temperature. Four genes showing distinctive expression patterns among samples were selected, and genes with expression patterns highly similar to those of these four genes were selected and grouped. An overlap analysis of the four groups was conducted using a Venn diagram. There was considerable overlap between Group1 (upregulation genes at both 20 and 30 ℃) and Group2 (upregulation genes at 30 ℃), which showed increasing trends at higher storage temperatures. There was almost no overlap among the other groups, suggesting that these groupings reflect the different biological statuses affected by storage temperature.