One embodiment of the present invention provides a method and a system for patching a set of objects containing references. The system uses a location structure to keep track of the locations of references within the set of objects. During the patching process, the system converts the references within the set objects from an absolute form into an offset-based form, where offsets are computed with respect to base addresses of objects. The system then applies an offset-based patch to the set of objects and to the location structure using a binary-patching technique. After applying the patch, the system converts the references in the set of objects back into absolute form. By using an offset-based patch, the system reduces the number of reference changes that need to be specified in the patch, thereby reducing the size of the patch.