We present a novel microstructure evolution model for PCFs in heating process, which is based on Navier-Stokes Equation in fluid mechanics and level set method. The model can be applied to describe microstructure deformation for PCFs. Utilizing the theoretical model, we have calculated accurate PCF microstructure changes from the different heating parameters, one of which may conduce an excellent microstructure for splicing, tapering, or else. The model is feasible in PCF optical devices design and manufacture without trial and error, which promotes the performance of PCFs partially. We have further performed a representative experiment on heated PCFs, and good agreements are found between experiment results and the simulations.