Intercalation is a robust method for tuning the physical properties of a vast number of van der Waals (vdW) materials. However, the prospects of using intercalation to modify magnetism in van der Waals (vdW) systems and the associated mechanisms have not been adequately studied. In this work, we modulated magnetic order in XY antiferromagnet NiPS₃ single crystals by introducing pyridine molecules into the vdW’s gap under different thermal conditions. X-ray diffraction measurements indicated pronounced changes in the lattice parameter β, while magnetization measurements at in-plane and out-of-plane configurations exposed reversal trends in the crystals’ Neél temperatures through intercalation/deintercalation processes. The changes in magnetic ordering were also supported by three-dimensional thermal diffusivity experiments. The preferred orientation of the pyridine dipoles within the vdW gaps was deciphered via polarized Raman spectroscopy. The results highlighted the relationship between the preferential alignment of the intercalants, thermal transport, and crystallographic disorder, along with the modulation of anisotropy in the magnetic order. DFT + U calculations indicated that the varying interlayer exchange interactions, regulated by intercalants, were responsible for modulating samples’ magnetic ordering. The study uncovers the possible merit of intercalation for manipulating spin orientations in spin electronics and advanced quantum devices.