To deal with the complexities associated with the rapid growth in a merged concept lattice, a formal method based on an entropy-based weighted concept lattice (EWCL) is proposed as a mechanism for merging multi-source geographic ontologies (geo-ontologies). First, formal concept analysis (FCA) is used to formalize different term-based representations in relation to the geographic domain, and to construct a merged formal context. Second, a weighted concept lattice (WCL) is applied to reduce the merged concept lattice, based on information entropy and a deviance analysis. The entropy of the attribute set is exploited to acquire the intent weight value, and the standard deviation contributes to computing the intent importance deviance value, according to the user preferences and interests. Some nodes of the merged concept lattice are then removed if their intent weights are lower than the intent importance thresholds specified by the user. Finally, experiments were conducted by combining fundamental geographic information data and spatial data in the hydraulic engineering domain from China. The results indicate that the proposed method is feasible and valid for reducing the complexities associated with the merging of geo-ontologies. Although there are still some problems in the application, the manuscript offers a new approach for the merging of geo-ontologies.