A full factorial experiment was conducted to analyze the main and interaction effects on the physical and mechanical properties of Cupressus funebris Endl. wood subjected to vacuum heat modification. The response variables evaluated were mass loss rate (ML, %), moisture resistance (MR, %), and modulus of rupture in bending (MOR, MPa). The results reveal significant variations in the effects of modification time, holding temperature, and vacuum pressure as independent factors, along with varying degrees of interaction effects among them. Simplifying the analysis model, a regression equation was derived to describe the relationship between the response variable (mass loss rate) and the factors: The model achieved an R-squared value of 96.0% and an R-squared (predicted) value of 73.7%, indicating good overall predictive performance. Optimal process parameters for mid-temperature vacuum heat modification of cypress were determined based on the mass loss rate and modulus of rupture (MOR), resulting in a modification temperature of 120 °C, holding time of 5 h, and a pressure intensity of 0.1. The reliability of the full factorial experiment was further confirmed through orthogonal testing.