This study presents a numerical investigation of the effect of decrease in water saturation of host rocks with dehydration reactions on the reconstruction of the thermal evolution of igneous-intrusions-bearing basins based on complex heat conduction models. The Bena 3 dike of Gippsland Basin (Australia) is selected as an example in this study. Results indicate: (1) the consideration of decrease in water saturation of host rocks (sandstone) with dehydration reactions in the models can obviously increase the predicted peak temperature Tpeak of host rocks. The corresponding maximum deviation of Tpeak occurs at the contact and reaches ~270 °C; (2) if water saturation of host rocks vary with dehydration reactions, the Tpeak can also be influenced by the quartz content of host rocks. The predicted Tpeak is higher for the host rocks with low quartz content. The maximum deviation of Tpeak caused by the quartz content can attain 115 °C. However, the deviation of Tpeak above 20 °C only occurs in a narrow region which is near the intrusion. Out of this region, the quartz content of sandstone has only a slight effect on Tpeak.