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In the rich phases of van der Waals (vdW) materials featuring intertwined electronic order and collective phenomena, characterizing elementary dynamics that entail the low-energy Hamiltonian and electronic degrees of freedom is of paramount importance. Here we performed resonant inelastic X-ray scattering (RIXS) to elaborate the spin-orbital ground and excited states of the vdW antiferromagnetic insulator FePS3, as well as their relation to magnetism. We observed the spectral enhancement of spin-orbital multiplet transitions about ∼ 100 and ∼ 220 meV, as well as quasielastic response, when entering the zig-zag antiferromagnetic phase, where the spectral changes develop an order-parameter-like evolution with temperature. By comparing with ligand field theory calculations, we discovered the essential role of trigonal lattice distortion and negative metal-ligand charge-transfer to account for these emergent excitations. Such spectral profiles are further examined upon confinement by mechanical exfoliation. We reveal their spectral robustness down to the few atomic layer limit, in accordance with the persistent antiferromagnetic state previously reported in optical measurements. Our study demonstrates the versatile RIXS capability that resolves magneto-crystalline anisotropy and charge-transfer energetics. These provide the crucial insight to understand how the spontaneous magnetic symmetry-breaking stabilizes in the quasi-two-dimensional limit for the vdW magnet FePS3.