Abstract: This study explored the effects of different storage temperatures on the postharvest quality of pepper fruits. A pepper cultivar (P1808) bred by the Zhejiang Academy of Agricultural Sciences was used in this study. Pepper fruits at the green ripe stage were collected and kept at room temperature (RT, 20 °C) or high temperature (HT, 30 °C) for 24 h and 48 h. Thereafter, the quality-related parameters of pepper fruits, including firmness, water loss rate, as well as contents of capsaicinoids, vitamin C, and amino acid, were analyzed. The results showed that under RT storage, the capsaicinoid content increased by more than 50% after 24 h and then decreased after 48 h, respectively; and the chlorophyll content decreased and remained at the same level after 24 h and 48 h, respectively; however, the water loss rate, relative electrolyte leakage, and protein content showed a tendency of continuous accumulation up to 48 h. Under the HT storage treatment, the capsaicinoid content gradually increased by approximately 50% and 150% after 24 h and 48 h, respectively; while the chlorophyll content continuously declined. After 48 h, the fruit firmness decreased significantly, while other parameters, including the water loss rate, malondialdehyde content, relative electrolyte leakage, and total carotenoid content, increased. The results of amino acid composition and nutritional value analysis of the pepper fruits under different temperature storage treatments showed that both the RT and HT treatments promoted the accumulation of 17 amino acids after 48 h. Further analysis based on the functional classification of amino acids indicated that the RT treatment significantly increased the content of total amino acids, essential amino acids, amino acids essential for children, and flavor-related amino acids. From the perspective of the nutritional value of amino acids, methionine and cystine were proved to be the main limiting amino acids in the pepper fruits; after 48 h, both the RT and HT storage treatments led to a decreased pattern of valine and isoleucine compared to the amino acid pattern spectrum in the pepper fruits. Ultimately, this study provides theoretical and practical guidance for postharvest maintenance of the quality of pepper fruits.