Employing exit-plane wave function (EPWF) reconstruction in high-resolution transmission electron microscopy (HRTEM), we have developed an approach to atomic scale compositional analysis of III-V semiconductor interfaces, especially suitable for analyzing quaternary heterostructures with intermixing in both cation and anion sub-lattices. Specifically, we use the focal-series reconstruction technique, which retrieves the complex-valued EPWF from a thru-focus series of HRTEM images. A study of interfaces in Al0.4Ga0.6As–GaAs and In0.25Ga0.75Sb–InAs heterostructures using focal-series reconstruction shows that change in chemical composition along individual atomic columns across an interface is discernible in the phase image of the reconstructed EPWF. To extract the interface composition profiles along the cation and anion sub-lattices, quantitative analysis of the phase image is performed using factorial analysis of correspondence. This enabled independent quantification of changes in the In–Ga and As–Sb contents across ultra-thin interfacial regions (approximately 0.6 nm wide) with true atomic resolution, in the In0.25Ga0.75Sb–InAs heterostructure. The validity of the method is demonstrated by analyzing simulated HRTEM images of an InAs–GaSb–InAs model structure with abrupt and graded interfaces. Our approach is general, permitting atomic-level compositional analysis of heterostructures with two species per sub-lattice, hitherto unfeasible with existing HRTEM methods.