Transparent MgAl2O4 ceramics were fabricated by using spark plasma sintering (SPS). The effects of annealing temperature on the optical and microwave dielectric properties were investigated by positron annihilation technique and X-ray photoelectron spectroscopy (XPS). The results showed that the optimal annealing temperature for the optical property improvement was 900°C and the in-line transmittance was improved to 74.9% at the wavelength of 550nm. The further elevation of annealing temperature damaged the optical performance due to the combination of oxygen vacancies. The Q×f values of transparent MgAl2O4 ceramics were an overall increase from 800°C to 1200°C, but decreased at 1300°C. It can be concluded that the annealing temperature plays an important role in the Q×f value, while a certain annealing temperature is corresponding to the best microwave dielectric property.