The mass shift of charmonium states in nuclear matter is studied in the perturbative QCD approach. The leading-order effect due to the change of gluon condensate in nuclear matter is evaluated using the leading-order QCD formula, while the higher-twist effect due to the partial restoration of chiral symmetry is estimated using a hadronic model. We find that while the mass of $J/\ensuremath{\psi}$ in nuclear matter decreases only slightly, those of $\ensuremath{\psi}(3686)$ and $\ensuremath{\psi}(3770)$ states are reduced appreciably. Experimental study of the mass shift of charmonium states in nuclear matter can thus provide valuable information on the changes of the QCD vacuum in nuclear medium.