A tunnel health monitoring (THM) system ensures safe operations and effective maintenance. However, how to effectively process and denoise several data collected by THM remains to be addressed, as well as safety early warning problems. Thus, an integrated method for Savitzky–Golay smoothing (SGS) and Wavelet Transform Denoising (WTD) was used to smooth data and filter noise, and the coefficient of the non-uniform variation method was proposed for early warning. The THM data, including four types of sensors, were attempted using the proposed method. Firstly, missing values, outliers, and detrend in the data were processed, and then the data were smoothed by SGS. Furthermore, data denoising was carried out by selecting wavelet basis functions, decomposition scales, and reconstruction. Finally, the coefficient of non-uniform variation was employed to calculate the yellow and red thresholds. In data smoothing, it was found that the Signal Noise Ratio (SNR) and Root Mean Square Error (RMSE) of SGS smoothing were superior to those of the moving average smoothing and five-point cubic smoothing by approximately 10% and 30%, respectively. An interesting phenomenon was discovered: the maximum and minimum values of the denoising effects with different wavelet basis functions after selection differed significantly, with the SNR differing by 14%, the RMSE by 8%, and the r by up to 80%. It was found that the wavelet basis functions vary, while the decomposition scales are consistently set at three layers. SGS and WTD can effectively reduce the complexity of the data while preserving its key characteristics, which has a good denoising effect. The yellow and red warning thresholds are categorized into conventional and critical controls, respectively. This early warning method dramatically improves the efficiency of tunnel safety control.