Misfit compounds are naturally stacked heterostructures, composed of layers with distinct sublattices. Owing to the incommensurate structural modulations and interlayer coupling, they can exhibit exotic phenomena such as Ising superconductivity and charge density waves. Here, we investigate the high-quality misfit superconductor (SnS)1.17NbS2, a non-centrosymmetric superconductor composed of alternating SnS2 and NbS2 layers. Utilizing scanning tunnelling microscopy, we obtained atomic-resolution images that clearly resolve, for the first time, both the square lattice on the SnS layer and the hexagonal lattice on the NbS2 layer. Spectroscopic imaging further reveal well-defined superconducting gaps on both layers, and visualizes its superconducting order parameter with atomic resolution, aiming to explore unconventional pairing enabled by the intrinsic structural modulations.