To ensure the long-term stable and uninterrupted service of satellite navigation systems, the robustness and reliability of time–frequency systems are crucial. Integrity monitoring is an effective method to enhance the robustness and reliability of time–frequency systems. Time–frequency signals are fundamental for integrity monitoring, with their time differences and frequency biases serving as essential indicators. These indicators are influenced by the inherent characteristics of the time–frequency signals, as well as the links and equipment they traverse. Meanwhile, existing research primarily focuses on only monitoring the integrity of the time–frequency signals’ output by the atomic clock group, neglecting the integrity monitoring of the time–frequency signals generated and distributed by the time–frequency signal generation and distribution subsystem. This paper introduces a time–frequency signal integrity monitoring algorithm based on the temperature compensation frequency bias combination model. By analyzing the characteristics of time difference measurements, constructing the temperature compensation frequency bias combination model, and extracting and monitoring noise and frequency bias features from the time difference measurements, the algorithm achieves comprehensive time–frequency signal integrity monitoring. Experimental results demonstrate that the algorithm can effectively detect, identify, and alert users to time–frequency signal faults. Additionally, the model and the integrity monitoring parameters developed in this paper exhibit high adaptability, making them directly applicable to the integrity monitoring of time–frequency signals across various links. Compared with traditional monitoring algorithms, the algorithm proposed in this paper greatly improves the effectiveness, adaptability, and real-time performance of time–frequency signal integrity monitoring.