Unrecoverable deformation or plasticity can be generated in crystalline metal-organic frameworks (MOFs) by compressive loading with different rates in various applications. Herein, plastic behaviors of MOF HKUST-1 crystals are investigated by a series of in situ strain-rate-dependent compression tests. The yield strength is found to significantly increase with increasing strain rate, following a logarithmic dependence. Our reactive molecular dynamics simulations illustrate that the yielding of crystalline HKUST-1 is induced by the irreversible collapse of its nanopores, which can be accelerated by thermal activation at finite temperatures. Based on this mechanism together with the reaction rate theory, we derive an analytical expression relating the yield strength of MOFs and strain rate, which fits experimental findings well. Overall, this work can expand our current understanding of MOF plasticity, which is of importance for the mechanical shaping and various applications of MOF crystals.