Abstract: To address the issue of structural heave at the tunnel floor in layered rock mass under high-stress conditions, a comprehensive control system combining engineering mitigation measures with structural parameter optimization was established. Numerical simulation techniques were employed to analyze the mechanisms of action and control effectiveness of these measures. The results indicate that installing radial anchor bolts and de-stressing holes at the tunnel floor effectively controls the heave of both the surrounding rock and the lining in this type of tunnel, while adding a buffer layer at the tunnel floor only has a limited effect on controlling lining heave; increasing the crown arch slenderness ratio and thickening the initial support of the crown arch have the most significant control effects on the invert of the heave structure, whereas measures to increase the strength of the initial support at the tunnel floor have limited inhibitory effects. Based on survey data from engineering case studies, this study provides recommended parameter values for two control measures—deepening the invert and thickening the initial invert support—under common operating conditions through computational analysis. These recommendations were successfully applied in the remediation of invert heave in a tunnel on the Chongqing-Guizhou Railway.