The aim of this study was to obtain molecular insight into the deactivation of recombinant urate oxidase (uricase, UOX, EC 126.96.36.199) (rUOX) from Aspergillus flavus. The enzyme is a tunnel-shaped homotetramer and has important clinical applications. By means of molecular dynamics simulations, multidimensional structural characterization and enzyme activity assays, we concluded that the thermal deactivation of UOX at neutral pH was associated with the loss of intersubunit hydrogen (H) bonds. This mechanism could also explain the deactivation of dilute aqueous UOX. Thermal deactivation of aqueous UOX due to dissociation of its subunits was ruled out. Displacement of H(2)O from the surface of UOX by less polar solvents such as methanol and dimethyl sulfoxide (DMSO) was proposed as an approach for strengthening intersubunit H bonds and consequently UOX stability. The effectiveness of this method was validated by both in silico and in vitro experiments. The results mentioned above provide insights for improving the stability of UOX and extending its applications. They may also be helpful for understanding the properties of other multimeric proteins.