The simulation of the growth stages of Myrica rubra in protected cultivation is a key aspect in understanding the interaction between the growth of the plant and environmental factors. To explore the impact of the microclimate in protected cultivation on the growth stages of Myrica rubra and accurately predict the evolution of these stages, this study utilized growth and development data of Myrica rubra from 2022 to 2024 in Lanxi of Zhejiang, along with concurrent meteorological data on light, temperature, and other factors. Three methods were employed for the growth stage simulation: growing degree day (GDD), physiological development time (PDT), and the clock model. The models were validated based on their performance. The results indicated that the clock model exhibited higher predictive accuracy and adaptability in simulating the various growth stages of Myrica rubra, particularly during the reddening stage and maturity stages, where the prediction errors were significantly smaller compared to GDD and PDT methods. The root mean square errors (RMSE) for the wintering, flowering, fruit setting, reddening stage, and maturity stages in the clock model were 2.83 d, 3.32 d, 4.24 d, 2.38 d, and 2.16 d, respectively. The normalized root mean square errors (nRMSE) were 0.47, 1.11, 0.47, 0.48, and 0.54, respectively. These results demonstrate that the clock model provides a more accurate reflection of the growth stage evolution of Myrica rubra, offering scientific support for optimizing cultivation management strategies. This can effectively promote the implementation of refined management practices, improving both management efficiency and effectiveness. In the future, the parameters of wintering period can be optimized and extended to multi-variety and multi-region applications.