The traditional freeze-drying process usually requires the insertion of a resistance temperature sensor (RTD) into the material to monitor the temperature variation and determine when drying has been achieved. However, this technique often causes damage to wooden relics in terms of conservation. In this study, we analyzed the real-time concentration of the dimensional stabilizer agent impregnation solution and were able to predict the end point of freeze drying in a nondestructive way. Using this method, we conserved 30 fragments of wooden structural components excavated at the Zhidanyuan Sluice Site of the Yuan Dynasty by vacuum freeze drying, achieving the desired effect of shape protection and ensuring the safety of these wooden components as well.