Radio frequency (RF) heating has been studied to inactivate bacteria in some powder foods. In this study, a 6 kW, 27.12 MHz RF system was used to pasteurize Salmonella in black fungus (Auricularia auricula) powder. The effects of different conditions (initial aw, electrodes gaps, particle sizes) on RF heating rate and uniformity were investigated. The results showed that RF heating rate was significantly ( p < 0.05) improved with decreasing electrodes gap and increasing initial aw, and the heating rate was the slowest when the particle size was 120–160 mesh. However, these factors had no significant ( p > 0.05) influence on heating uniformity. RF pasteurization of Salmonella in black fungus powder was also studied. The results showed that, to inactivate Salmonella for 5 log reductions in the cold spot (the center of surface layer), the time needed and bacteria heat resistance at designated temperature (65, 75, 85 °C) decreased with increasing aw, and the first order kinetics and Weibull model could be used to fit inactivation curves of Salmonella with well goodness. Quality analysis results showed that although RF pasteurization had no significant ( p > 0.05) effect on Auricularia auricula polysaccharide (AAP) and total polyphenols, obvious changes were found on color. Results suggested that RF pasteurization can be considered as an effective pasteurization method for black fungus powder.