High-spatiotemporal-resolution land surface temperature (LST) data are crucial for analyzing surface energy balance, modeling temperature-related processes, and monitoring thermal environments. However, despite advancements in multi-source fusion and reconstruction techniques, high-frequency LST data remain susceptible to anomalies such as abrupt changes and outliers due to retrieval uncertainties and varying observation conditions. Conventional statistical outlier detection methods risk misidentifying physically plausible rapid weather changes as data errors, introducing systematic biases. To address this, we propose a two-stage anomaly detection framework that follows a “temporal physical pre-screening first, spatial statistical verification later” logic. First, a piecewise empirical model, based on typical diurnal LST variation characteristics, is constructed to identify points violating physical patterns. Subsequently, a spatial consistency test using median absolute deviation (MAD) is introduced to distinguish real weather-driven fluctuations from genuine data anomalies from a spatial synergy perspective. This sequential design effectively reduces the risk of mis-correcting physically reasonable temperature variations. Validated using hourly seamless LST data (2016–2021) and ground observations in the Heihe River Basin, our method outperformed Seasonal-Trend decomposition using Loess (STL), double standardization methods, and robust Holt–Winters. For over 87% of the detected anomalies, the proposed method demonstrated positive improvement rates in RMSE, MAE, R, and R². The overall average improvement rates reached 23.61%, 18.79%, 16.46%, and 61.33%, respectively, indicating robust performance. The results underscore that explicitly incorporating physical constraints enhances the reliability and interpretability of quality control for high-temporal-resolution remote sensing LST data.