Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present the stratum-adjusted correlation coefficient (SCC), a reproducibility measure that accounts for these features. SCC can assess pairwise differences between Hi-C matrices under a wide range of settings and can be used to determine optimal sequencing depth. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The R package HiCRep implements our approach.