We present accurate quantum dynamics calculations on vinylidene-d2 (fully deuterated vinylidene) isomerization. This is achieved by large-scale parallel computations with an efficient theoretical scheme developed by us in which basis functions are customized for the deuterium migration process. Mode-specific permutation tunneling splittings of vinylidene-d2 states are reported here for the first time, and evident isotope effects are revealed. The A1 ', B2 ', A1 ″, and B2 ″ symmetric vinylidene-d2 states are calculated, and the peaks recently observed in the cryo-SEVI spectra are analyzed, with very good agreement between theory and experiment achieved for the energy levels. In addition, a few vinylidene-d2 states beyond the experimental energy region are reported. Our studies are helpful for acquiring a better understanding of isotope effects in the double-hydrogen migration processes.