[110] images are taken for 3C-SiC/(001)Si hetero epitaxial films containing small-angle grain boundaries by using a 200 kV LaB6 filament high-resolution transmission electron microscope. Deconvolution processing is performed to transform the experimental images which do not represent intuitively the projected crystal structure into structure images. First, Si and C atomic columns with a distance of 0.109 nm are resolved in a perfect structure image region, and then recognized from each other by analyzing the image contrast change with sample thickness based on the pseudo-weak phase object approximation. Subsequently, two complex dislocation cores located in the vicinity of small-angle grain boundaries are obtained at an atomic level, and the atomic structure models are constructed and confirmed by matching the experimental images with the simulated ones. Hence, the atomic configurations of dislocation cores are derived from only a single experimental image with the average structure of perfect crystal known in advance. The formation of small-angle grain boundaries in 3C-SiC/Si with the occurence of complex dislocations in their vicinity is discussed.