This paper reports an investigation of the influences of surface effects and residual stress on the quality factor of a circular microdiaphragm in contact with liquids on one side. Acoustic radiation, as the main source of energy dissipation, can decrease the quality factor of a circular microdiaphragm. An approximate solution for the natural frequency can be obtained based on the Rayleigh–Ritz energy method. The results show that the influence of surface effects on the quality factor is obvious, in particular for thinner microdiaphragms. A stiffened surface decreases the quality factor, while a softened surface increases it. Furthermore, the quality factor increases with increases in the normalized tension parameter k for both stiffened and softened surfaces. If k is greater than 30, the influence of the surface effects on the quality factor must be considered. The results can provide effective guidance for the determination of dimensions and selection of material parameters in designing microdiaphragm resonant sensors.