Mountainous settlements accommodate nearly one tenth of the world’s population. Most mountainous cities have adopted the strategy of polycentric urban development due to an asymmetric geography, which has received little attention from mainstream research. To fill the research gap, we proposed an analytical framework and conducted a multi-dimensional measurement of polycentricity. Taking Chongqing for the case study, this work confirmed that polycentricity is morphological and functional in mountainous cities. Polycentricity is believed to be particularly applicable to mountainous and water-rich landscapes, leading to an appropriate, balanced distribution and the strong multi-directional connectivity of urban nodes. This characteristic may partly result from natural determinism and long-term planning adaptation, complementary to market forces. Policy implications for planning such as avoiding excessive encroachment on natural barriers and increasing functional linkage in newly established subcenters were also proposed.