Comparing innovation across regions is challenging. Innovation processes and outcomes are shaped by different actors, interactions, and institutions. Regional contingencies complicate the comparison as evident from the existing approaches to explaining innovation across regions. Quantitative innovation measurement approaches may quantify differences between regions, but disregard regional contingencies. Qualitative, heuristic approaches may understand an individual region’s innovation history and culture, but cannot quantify differences between regions. This paper introduces an adapted version of the analytical hierarchy process (AHP) to fill this methodological void. It shows that the AHP allows us both to consider regional contingency and to quantify differences between regions. This paper applies the AHP to compare innovation of the equipment manufacturing industries of Shanghai and Xiamen, China. It thus exemplifies how this method might be used for research and application in human geography, planning, regional science, and related fields.