For a 7 nm technology node and beyond, multi-beam mask fabrication based on charged particles has attracted attention widely and shows great advantages in terms of throughput. However, the heating effect during mask writing is a serious problem and makes deformation error. To address this issue, an accurate analysis of heating with multi-beam writing is necessary. In this study, the thermal effects of electron beams on a mask during writing time (exposure time and nonexposure time) were simulated with a finite element numerical method. The variation in the temperature field with two writing paths (S-shaped and E-shaped) was analyzed. A comparative analysis of the mask’s deformation under different writing paths was conducted. Numerical research shows that the thermal analysis method in this study provides a guide for optimizing the process parameters of mask fabrication.