We perform the first simultaneous global QCD extraction of the transverse momentum dependent (TMD) parton distribution functions and the TMD fragmentation functions in nuclei. This analysis allows us to extract the three-dimensional information of the partonic structure of nuclei as well as the three-dimensional information for hadron formation in a nuclear medium. In this analysis, we take into account the world data from semi-inclusive electron-nucleus deep inelastic scattering and Drell-Yan type di-lepton production in proton-nucleus collisions, comprising a total of 126 data points from 6 data sets with $\chi^2/dof = 1.045$. We quantify for the first time the broadening of partonic distributions in nuclei comparing with those in free nucleons. We also make predictions for the ongoing JLab 12 GeV program and future EIC measurements, which are expected to further constrain the three-dimensional partonic structure of nuclei.