The morphology of the nanocrystals is a critical parameter for determining their performance in particular applications. In our experimental work, ZnWO₄ nanocrystals with different morphologies are synthesized by the hydrothermal method. It has been found that the shape of ZnWO₄ nanocrystals is strongly dependent upon the pH of the growth solution. Combining the experimental findings, first-principles calculations are used to investigate the microscopic mechanism of morphology transformation of ZnWO₄ nanocrystals controlled by surface chemistry. Surface structures, surface energies and surface tensions of several low-index surfaces of ZnWO₄ under the different surface passivated conditions are examined. The surface energies of (010) and (011) facets are increased when the fraction of hydroxyl in the adsorbates is increased. The (100) surface is consistently the highest energy surface except for the most-basic conditions. According to the Wulff law, the equilibrium shapes of ZnWO₄ nanocrystals are obtained from the respective surface energies. Our results show that the effect of surface chemistry on the morphology of ZnWO₄ nanocrystals is apparent. The aspect ratio of the nanocrystals is reduced gradually when the basicity of the surface conditions is increased, which is consistent with our experimental findings. A modified Wulff construction model which considers the effect of surface tension draws the same conclusions. Our investigations are meaningful to gain further understanding of how to achieve shape-controlled nanocrystal synthesis by tuning the surface chemistry.