Unconventional superconductivity in heavily boron-doped nanocrystalline diamond films (HBDDF) produced a significant amount of interest. However, the exact pairing mechanism has not been understood due to a lack of understanding of crystal symmetry, which is broken at the grain boundaries. The superconducting order parameter (Δ) of HBDDF is believed to be anisotropic since boron atoms form a complex structure with carbon and introduce spin-orbit coupling to the diamond system. From ultra-high resolution transmission electron microscopy, the internal symmetry of the grain boundary structure of HBDDF is revealed, which can explain these films’ unconventional superconducting transport features. Here, we show the signature of the anisotropic Δ in HBDDF by breaking the structural symmetry in a layered microstructure, enabling a Rashba-type spin-orbit coupling. The superlattice-like structure in diamond describes a modulation that explains strong insulator peak features observed in temperature-dependent resistance, a transition of the magnetic field-dependent resistance, and their oscillatory, as well as angle-dependent, features. Overall, the interface states of the diamond films can be explained by the well-known Shockley model describing the layers connected by vortex-like structures, hence forming a topologically protected system.