The present invention relates to a missing tag uncertainty parallel detection method of an anonymous multi-group radio frequency identification system. The method comprises: a reader calculates an optimal detection turn r and the frame length fk of a current k turn under the condition that the detection reliability degree of an anonymous multi-group radio frequency identification system is satisfied; the reader predicts the state of each time slot, detects the actual state of each time slot and determines whether a corresponding group has missing tags or not through comparison of the discrimination between the prediction state and the actual state; and if the reader detects that all the groups have missing tags, the reader stops detection, or else, the reader completes the execution of the remaining r-k turn, and completes the missing tag parallel detection of the whole anonymous multi-group radio frequency identification system. The missing tag uncertainty parallel detection method of the anonymous multi-group radio frequency identification system can realize parallel missing tag detection of multi-group tags to effectively protect tag privacy and effectively reduce the detection time and improve the detection efficiency on the premise of ensuring the detection reliability degree required by the anonymous multi-group radio frequency identification system.