Non-stoichiometric ceramic samples of Mn0.97WO4 and MnW0.97O4 were prepared by a solid-state reaction to study the effects of vacancies at different lattice positions on the structure and properties of MnWO4 materials caused by non-stoichiometric. Positron annihilation technology was introduced to study the vacancy characteristics of the MnWO4, Mn0.97WO4, and MnW0.97O4 ceramics. The results indicated that non-stoichiometric did not affect the monoclinic lattice structure of any of the MnWO4 samples, and had no obvious effect on the lattice parameters of the samples. The analysis of positron annihilation lifetime spectroscopy showed that W vacancies were the main defects in MnW0.97O4 samples, and Mn vacancies were favored in Mn0.97WO4 samples, the vacancies concentration for non-stoichiometric MnWO4 samples was higher than that of stoichiometric MnWO4. It was observed that the magnetization and transition temperatures of the non-stoichiometric MnWO4 system were increased, and the temperature range in which AF2 phase existed was enlarged. This study demonstrated that non-stoichiometric could enhance the magnetic properties of MnWO4, the effect of Mn vacancy on the properties of MnWO4 is higher than that of W vacancy. The intimate correlation between the vacancy defects and magnetic properties provides us strong evidence that the magnetic properties of MnWO4 can be enhanced by regulating vacancy defects.