More accurate, spatio-temporally, and physically consistent LST estimation has been a main interest in Earth system research. Developing physics-driven mechanism models and data-driven machine learning (ML) models are two major paradigms for gapless LST estimation, which have their respective advantages and disadvantages. In this paper, a physics-constrained ML model, which combines the strengths in the mechanism model and ML model, is proposed to generate gapless LST with physical meanings and high accuracy. The hybrid model employs ML as the primary architecture, under which the input variable physical constraints are incorporated to enhance the interpretability and extrapolation ability of the model. Specifically, the light gradient-boosting machine (LGBM) model, which uses only remote sensing data as input, serves as the pure ML model. Physical constraints (PCs) are coupled by further incorporating key Community Land Model (CLM) forcing data (cause) and CLM simulation data (effect) as inputs into the LGBM model. This integration forms the PC-LGBM model, which incorporates surface energy balance (SEB) constraints underlying the data in CLM-LST modeling within a biophysical framework. Compared with a pure physical method and pure ML methods, the PC-LGBM model improves the prediction accuracy and physical interpretability of LST. It also demonstrates a good extrapolation ability for the responses to extreme weather cases, suggesting that the PC-LGBM model enables not only empirical learning from data but also rationally derived from theory. The proposed method represents an innovative way to map accurate and physically interpretable gapless LST, and could provide insights to accelerate knowledge discovery in land surface processes and data mining in geographical parameter estimation.