The defects and heterogenous structures which are far beyond the molecular scale always exist on the film surfaces or inside the films, such as surface defects, phase separation, crystallization, microbubbles and other impurity particles, resulting in the significant decline of their performance. Until now, in-situ characterization of these defects and structures is still challenging. Herein, we explore the applications of the digital holographic microscope (DHM)??, an in-situ, nondestructive and high-precision optical 3D imaging technique, in the 3D characterizations of both the surface and internal defects of polymer films. Examples include 3D distribution characterization of 100 nm polystyrene nanoparticles in a thin liquid layer, morphology of the surface of the polyurethane coated wafer, phase separation process of polymethacrylate film from water, edge crystallization monitoring during the drying of polyethylene glycol film, and characterization of micro-nano bubbles in the polyvinyl alcohol film. Obviously, DHM has unique advantages and is promising for future applications in polymer film characterization.