Due to their radical character, paramagnetic endohedral metallofullerenes (EMFs) are prone to dimerize. The dimerization exhibits high selectivity, i.e., only one or a few dimer structures, among a great number of possible choices of carbon cage forms and reaction sites, were observed in experiments. To unravel the determining factors of dimerization selectivity, we conducted a systematic computational study of the dimerization of a series of experimentally synthesized paramagnetic EMFs, representatively including M@C-82 (M = Y, Sc, La), La@C-72 with adjacent pentagons, and Y-2@C-80 in triplet state. By exploring many possible monomer structures and all possible dimerization sites for each monomer, we can explain the unique dimer structure of Y@C-82 observed in the experiment. Thereby, we suggest two energetic criteria to determine whether a dimer structure can be formed under certain synthetic conditions: the monomer precursor should be sufficiently stable and the dimerization process should be sufficiently exergonic. Furthermore, we show that commonly used reactivity descriptors, based on different physical arguments such as spin density, geometric characteristics, aromaticity, and bond orders, all have poor or no correlation with the dimerization regioselectivity of EMFs. Conversely, we propose a simple hydride model able to quantitatively predict the relative dimer energies, which would serve as reliable and general guidance for the dimerization of EMFs and their derivatives.