Heat transfer problem is very important in fusion splicing process of photonic crystal fibers (PCF) due to the potential distortion which can be introduced when exposing the structure to high temperature. Such heating is further complicated to internal air-structures of PCF. The heat transfer of fusion splicing PCF and theorize for confirming the optimal fusion splicing conditions are investigated. Based on heat transfer and conservation law of energy, a three-dimensional axisymmetric conductive heat transfer model is built using a CO₂ laser as heat source, the transient heat transfer in fusion splicing process of PCF is simulated in order to avoid collapsing the air holes. Experiments and analysis shows that the heat transfer model may find out heat transfer characteristic of PCF fusion splicing process, and provide theory basis for confirming optimal fusion splicing conditions.