Utilizing presynthesized large Na2Ni12Ln2 clusters (Ln = Dy and Tb) supported by calixarene as molecular building blocks (MBBs), we have obtained a series of cationic trigonal prismatic heterometallic organic nanocages (HMONCs) with tunable sizes through a stepwise method. Specially, in each structure of the HMONCs, three linear dicarboxylate linkers substitute the peripheral coordinated acetate ligands of two Na2Ni12Ln2 clusters to form an unprecedented Na4Ni24Ln4 HMONC through a M2L3 condensation. Moreover, magnetic study reveals that the Na2Ni12Dy2 core retains its slow magnetic relaxation behavior. Gas sorption behaviors of these HMONCs were also studied. To the best of our knowledge, these HMONCs built from large heterotrimetallic Na2Ni12Ln2 MBBs, which are based on smaller Ni4-calix ones, have not been reported in any other cages to date. In addition, this research also provides a new strategy for the design and construction of HMONCs with predictable structures and functional properties.