Bougainvillea, a widely used ornamental plant, is mainly propagated by cuttings and tissue culture. Still, large-scale production of Bougainvillea is often difficult because of rooting issues. Therefore, based on an early establishment of the regeneration system for tissue culture in Bougainvillea by our research team, we further studied its rooting mechanism. It was observed that the morphology and anatomical structure of Bougainvillea buttiana ‘Miss Manila’ contained endogenous hormones, such as indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellic acid (GA3), and zeatin-riboside (ZR), including peroxidase (POD), polyphenol oxidase (PPO), and IAA-oxidase (IAAO) activities. Following the culture, Days 0–15 consisted of the induction and initiation stages, while Days 15–25 included the expression stages. No latent root primordium was found in the Bougainvillea plantlet, which belonged to the induced rooting type. The root primordium was derived from callus cells generated by divisions of parenchyma cells in the basic tissues. It was found that the changes in the POD, PPO, and IAAO activities were closely related to the formation of adventitious roots (AR), in which the highest rooting values occurred during the transition from the initiation stage to the expression stage, whereas the endogenous IAA and ABA contents had negative and positive correlations during the induction, initiation, and expression stages.; The values of GA3 and ZR also peaked during the transition from the initiation to the expression stage. ZR and GA3 were found to promote adventitious root formation, while ABA inhibited it. The IAA/ABA, ABA/ GA3, and IAA/ZR ratios also shifted at the onset of the expression stage of AR, indicating these values were closely related to their occurrence. Overall, this study provides the basis for further research considering AR formation in Bougainvillea, and the propagation of various Bougainvillea varieties.