The essential work of fracture (EWF) method is widely used in the experimental characterization of fracture toughness of thin polymer films. However, the underlying physics of this method and the EWF parameters are not completely understood. In the present work, we investigated the correlations between the EWF parameters and the molecular structures of amorphous and ductile polymers. Based on our experimental observations, a physical model describing the EWF method on the molecular level was built. With this model, the variations of the EWF parameters with extrinsic and intrinsic factors under a plane stress condition were explained successfully; the theoretical values estimated with some assumptions and approximations of the EWF parameters agree satisfactorily with the experimental ones. This is the first theoretical model in the development history of the EWF method, which gives reliable physical meanings of the EWF parameters. The precise description of the molecular structure and fracture toughness relationships given by this model can also provide guidelines to molecular design of new polymers with high toughness.