Longan polyphenoloxidase (PPO) was extracted and partially purified using ammonium sulfate precipitation and dialysis. The PPO characterizations were compared using endogenous substrate (-)-epicatechin and exogenous substrate catechol. The optimal pH and optimal temperature for the PPO activity were different when reacting with both substrates. The addition of ethylenediaminetetraacetic acid disodium salt into both substrate-enzyme systems exhibited the same lowest inhibition of the PPO activity. L-ascorbic acid and L-cysteine were the best inhibitors to endogenous substrate-enzyme system, while L-ascorbic acid and glutathione were most effective inhibitors to exogenous substrate-enzyme system. Cupric (Cu2+), ferric (Fe3+), and ferrous (Fe2+) ions accelerated the enzymatic-catalyzed reactions of both substrates. Kinetic analysis indicated that longan PPO strongly bound endogenous substrate but possessed a higher catalytic efficiency to exogenous substrate, and moreover, (-)-epicatechin was determined as the optimal substrate for longan PPO. This study is useful to exactly illuminate the enzymatic-catalyzed browning mechanism of postharvest longan fruit.