The polyvinylidene difluoride molecular crystal structure had been studied by middle infrared (MIR) spectroscopy. The crystal structure of polyvinylidene difluoride molecular included α crystal structure, β crystal structure and γ crystal structure. Temperature-dependent middle infrared (TD-MIR) spectroscopy and two dimensional middle infrared (2D-MIR) spectroscopy of polyvinylidene difluoride molecular were studied also. In the (303~433 K), (433~453 K) and (453~ 523 K) temperature range, with the increase of the temperature, the corresponding frequency and absorption intensity of polyvinylidene difluoride molecular crystal structure had changed obviously, the crystal structure of polyvinylidene difluoride molecular showed different sensitivity and order to the heat, and the crystal structure interchange mechanism were studied furthermore. The paper demonstrated the key roles of three-step MIR spectroscopy in the analysis of crystal structure and thermal denaturation of the important functional polymer materials with piezoelectric properties (polyvinylidene difluoride).