Spermidine is one of the secondary metabolites (SM) related to plant tissue browning caused by chilling, but whether it plays a role in pineapple internal browning (IB) occurred at ambient temperature remains unknown. In this study, pineapples affected by severe IB after 9-d storage showed dramatic changes in SMs, with 94.94% of 79 being upregulated. Among the 4 downregulated were spermidine. Exogenous abscisic acid (ABA) suppressed and gibberellin (GA3) aggravated IB and they differentially regulated SMs and spermidine. Compared with the control, ABA downregulated 65 of 70 SMs and upregulated spermidine, while GA3 upregulated 7 of 24 SMs and did not obviously affect spermidine. Exogenous spermidine alleviated IB, confirming the role of spermidine in regulating IB. ABA upregulated spermidine biosynthesis genes AcARG1 and AcSPDS, while GA3 upregulated AcPAO2. ABA downregulated and GA3 upregulated SAM, ACS and ACO. ABA reduced 1-aminocyclopropane 1-Carboxylate (ACC) and GA3 did not. ABA upregulated NCED, ABA2 and AAO3 and increased endogenous ABA, while GA3 showed opposite effects. Collectively, the findings indicate spermidine play an important role in regulating IB of pineapple. Moreover, this work may provide novel insight into the mechanism underlying interactions of spermidine with ABA and GA in regulating quality of harvested fruit.