Studies on structural orientation of polymers near the surface and interface or in confined geometry mostly dealt with the resulting anisotropic arrangements of the involving polymer molecule. The molecular dynamics during the orientation process of a target polymer was, however, not concerned so far. In the present study, molecular orientation of poly(ethylene 2, 6-naphthalate) (PEN) thin films during isothermal and nonisothermal crystallization was investigated by the combination of in situ reflection-absorption infrared spectroscopy (RAIR) and grazing incidence X-ray diffraction (GIXD) techniques. The results disclose that the naphthalene ring and CO in PEN molecule is prone to alignment parallel to the film surface during the formation of alpha-form crystalline. In situ RAIR measurements further suggest that the kinetics of molecular orientation exhibits clearly different from that of crystallization. In situ GIXD experiments done by synchrotron radiation also reveal the structural developing process during the orientation, in which the naphthalene ring rotates to be more parallel to the surface than the lattice plane containing b and c axes. Furthermore, the possible mechanisms for the observed orientation in PEN thin films are also discussed.