Pepper plants are subject to complex environmental factors including abiotic and biotic stresses in fields, as well as the significant effects of climate changes, including low and high temperatures. Low temperature stress in the growth and development of pepper plants is one of the most critical issues, and directly impacts the crop yield and productivity of pepper plants. Therefore, it is essential to select and breed low temperature-(LT) tolerant pepper (Capsicum annuum L.) cultivars. This research was conducted to assess the agronomical traits of 39 pepper accessions belonging to the chili and bell fruit varieties which were cultivated under two different night temperature set-points: at 15 °C for a suboptimal temperature (CT) and at 10 °C for a low temperature (LT). The plant heights (PH) of most pepper accessions in a LT were significantly decreased compared to those in a CT. The stem diameter (SD) and the length of main axis (LMA) varied depending on the genotypes under LT. Moreover, the number of flowers (NFL), total number of fruits (NFR), fruit yield (FY), fruit fresh weight (FFW), fruit length (FL), fruit diameter (FD), and number of seeds in a fruit (NSF) remarkably declined in a LT compared to in a CT. The evaluated agronomical traits between LT and CT were further applied for the correlation analysis, principal component analysis (PCA), and hierarchical cluster analysis. Notably, the FY trait was correlated with other reproductive traits including NFR, FFW, FD, and FL on the positive directions and thirty-nine LT-treated pepper accessions were clustered into seven groups by the hierarchical clustering analysis. The selected accessions were primarily involved in the positive trends with the reproductive index including NFR, FL, FD, and FFW traits and could be used for pepper breeding programs to develop LT-tolerant cultivars.