Due to the potential applications in next‐generation micro/nano electronic devices and functional materials, magnetic germanium (Ge)‐based clusters are receiving increasing attention. In this work, we reported the structures, electronic and magnetic properties of CrMnGen with sizes n = 3–20. Transition metals (TMs) of Cr and Mn tend to stay together and be surrounded by Ge atoms. Small sized clusters with n ≤ 8 prefer to adopt bipyramid‐based structures as the motifs with the excess Ge atoms absorbed on the surface. Starting from n = 9, the structure with one TM atom interior appears and persists until n = 16, and for larger sizes n = 17–20, the two TM atoms are full‐encapsulated by Ge atoms to form endohedral structures. The Hirshfeld population analyses show that Cr atom always acts as the electron donor, while Mn atom is always the acceptor except for sizes 3 and 6. The average binding energies of these clusters increase with cluster size n, sharing a very similar trend as that of CrMnSin (n = 4–20) clusters, which indicates that it is favorable to form large‐sized clusters. CrMnGen (n = 6, 13, 16, 19, and 20) clusters prefer to exhibit ferromagnetic Cr–Mn coupling, while the remaining clusters are ferrimagnetic.