Heat transfer problem is very complicated in fusion splicing process of photonic crystal fibers (PCFs) due to different of air hole that may require different fusion splicing power and location of heat source. Based on study on heat transfer characteristic of fusion splicing PCFs, the optimal offset in fusion splicing process is researched by a three-dimensional conductive heat transfer model. According to theory and experimental analysis results: this method may be applied to compute the optimal fusion splicing conditions between PCFs and SMFs, which may obtain a lower fusion splicing loss.