The invention relates to a conflict shifting processing method for multi-source spatial data combination. The method comprises the following steps of: (1) reading data, and constructing topological relationships among entities; (2) performing entity matching; (3) performing the regulation and combination of entity coordinates; (4) checking whether combination results comprise mismatching or not, correcting the mismatching and returning to the step (3) if the combination results comprise the mismatching, and executing the step (5) if the combination results do not comprise the mismatching; and (5) automatically detecting the existence or inexistence of a picture conflict, and if the picture conflict is automatically detected, performing conflict shifting by adopting a least square adjustment method. Compared with the prior art, the method has the advantages of saving manpower and material resources, eliminating differences among data sets, solving the spatial conflict, maintaining geometrical characteristics of the entities, and the like.