Three cultivars of green pepper with unique fruit shapes, 'Kkwariput', 'Gilsang', and 'Cheongyang', were investigated for changes in physiology and functional compounds during storage to optimize postharvest management. The results showed that the respiration and ethylene production rates of 'Gilsang' were lower than those of 'Kkwariput' and 'Cheongyang', having the lowest weight loss during storage at both 4℃ and 20℃. The 'Cheongyang' pepper exhibited the highest firmness among the three cultivars, and it remained high until the end of storage. The soluble solids content and the titratable acidity were significantly higher in 'Cheongyang' than in 'Gilsang' and 'Kkwariput'. With regards to fruit color, in all three cultivars the L* values decreased while the a* values increased with storage time. Based on the appearance index, 'Cheongyang' had a longer shelf life at 20℃ than 'Gilsang' or 'Kkwariput'. However, 'Gilsang' showed the lowest seed browning rate at 5 day at 20℃ among the three cultivars after 14 day of cold storage at 4℃. The results of functional compounds analysis showed that capsaicin content increased with storage time, with the highest content found in 'Cheongyang'. Antioxidant capacity, as determined by ABTS and DPPH assays, increased with storage time, and 'Cheongyang' showed higher antioxidant retention capacity than 'Gilsang' and 'Kkwariput'. The highest vitamin C content was also found in 'Cheongyang'. Based on the overall superior results of the 'Cheongyang' cultivar, this study suggests a close correlation between the retention capacity of functional compounds and the shelf life in green peppers.