Enzymatic browning is a major issue that reduces the commercial value of Luffa cylindrica during storage, processing, and transportation. Our results showed that 1% CaCl2 treatment was optimal for reducing the surface browning of fresh-cut luffa. After storage at 25 °C for four days, the treated luffa had a significantly higher total phenolic (TP) content than the untreated luffa. At the end of the storage period, the calcium treatment showed low malondialdehyde (MDA) and hydrogen peroxide (H2O2) accumulation in the luffa. The treated luffa maintained higher superoxide dismutase (SOD), catalase (CAT), and phenylalanine ammonia lyase (PAL) activities and lower polyphenol oxidase (PPO) activity as compared to the untreated luffa. Furthermore, the genes regulating SOD (e.g., SOD1, SOD2, and SOD3), CAT (e.g., LcCAT1 and CAT2), and PAL (e.g., PAL1 and PAL2) in calcium-treated luffa were upregulated to varying degrees, suggesting that Ca2+ inhibited the browning of fresh-cut tissue by regulating the activities of those enzymes. Ultrastructure images showed that the treated luffa could maintain the relative integrity of the cell membrane and organelles. Therefore, Ca2+ might act as a second messenger to reduce ROS oxidative damage and maintain the cell membrane integrity. This study provides new insights into the breeding of new luffa varieties that are resistant to browning and post-harvest treatments to reduce the browning of luffa tissue.