Background: Autoclaving is used to eliminate contamination during tissue culturing, however, it is a complicated process, time-consuming and costly. Chemical sterilization of tissue culture can effectively eliminate contamination, is a simple procedure, and cost effective. However, studies on the chemical sterilization mostly focus on bud induction, while the effects of chemical sterilization overall process of tissue culture, including bud induction, proliferation, and rooting, remain to be determined. Here, we investigate the effect of chemical sterilization on bud induction, proliferation, and rooting of Acacia mangium × A. auriculiformis.Results: The results showed that chlorothalonil (0.2 g/L) was a suitable chemical sterilant, and bud induction medium was 1/8 Murashige and Skoog medium + agar 7 g/L + chlorothalonil 0.2 g/L + 6-benzylaminopurine 0.5 mg/L The highest induction rate (99.54%) was observed in the third to fifth buds’ stem segments collected in October treated with 0.8 g/L carbendazim for 3 min, with a contamination rate of 0. The rooting medium was agar 7 g/L + chlorothalonil 0.2 g/L+ indolebutyric acid 1.5 mg/L + naphthylacetic acid 0.5 mg/L, and the rooting rate was 97.62%. The proliferation rate and subculture duration showed a positive correlation, while the proliferation rate was 3.58 times higher at the fourth subculture rooting. Conclusions: Our results suggest that chlorothalonil can effectively replace autoclaving during bud induction, proliferation, and rooting of A. mangium × A. auriculiformis. The findings of this study provide technical support for rapid seedlings propagation, accelerates the breeding process of Acacia, and can be applied in other tree species.