Abstract Background Heat treatment is widely used to break dormancy for seed germination and phytohormones could be deeply involved. However, effect of heat treatment on phytohormone related genes/proteins/metabolites and possible relationship with dormancy release remains unclear in oil palm. In this study, oil palm seeds were heat-treated at 39 °C for 60 days according to the method for commercial production. The embryos of seeds during heat treatment (0 d, 15 d, 30 d, 45 d and 60 d) and of germinated seeds (70 d and 75 d) were selected to discover the mechanisms involved in oil palm seed germination. RNA-seq and iTRAQ were applied to investigate DEGs and DEPs related to seed germination; qPCR and western blot were used as validation accordingly; endogenous phytohormones were determined by LC-MS/MS and exogenous phytohormones were also applied to validate their effects on seed germination. Results RNA-seq results showed that plant hormone signal transduction was one of the most important pathways and eight phytohormones involved, while six of them (ABA, GA, ET, CTK, IAA and JA) were also identified by iTRAQ. Both RNA-seq and iTRAQ results showed that the expression of ABA decreased after heat treatment, which was further validated by qPCR and western blot. Furthermore, changes in endogenous phytohormones showed that ABA decreased rapidly to about 9% of the control at 30 d and then stayed at very low levels until germination; GA and CTK increased while IAA was not affected by heat treatment. Besides, exogenous ABA treatments (10, 100, 1000 mg/L) showed that the germination rate decreased to 63, 42 and 16% of the control, respectively, suggesting that ABA suppress seed germination and the inhibition effect increase with higher concentration; while the germination rates of exogenous GA and IAA treatments barely changed among different concentrations. Conclusions Phytohormones are deeply involved in oil palm seed germination and ABA acts as an inhibitor. Heat treatment can eliminate endogenous ABA and break dormancy, while GA and CTK may also involve in dormancy release. At least 30 days of heat treatment might be necessary. This study provided informative perspectives on oil palm seed germination, which could be also applicable in other palm species.