AbstractSymmetries in nanoscale structures can be decisive for their structural, electronic, and magnetic properties, particularly in systems with reduced dimensions. Here we show that the symmetries of a flat metal-organic molecule adsorbed on a transition metal dichalcogenide, a 2-dimensional layered material, have a dramatic effect on the total spin and the intramolecular spin-spin interactions. Using a scanning probe microscope, we find two different molecular spin states by modifying the symmetry of the molecules via the twist angle to the substrate. Additionally, we observe significant non-collinear Dzyaloshinskii–Moriya interaction between two electron spins on the molecule induced by the spin-orbit coupling of the van der Waals coupled layered material with broken inversion symmetry. Our work opens a path for modifying the spin by exploiting symmetries and for studying the nature of surface-induced non-collinear spin-spin interaction within a single molecule which might allow the realization of more complex topological spin structures.