The rudder surfaces and lifting surfaces of a missile are utilized to acquire aerodynamic forces and moments, adjust the missile’s attitude, and achieve precise strike missions. However, the harsh flying conditions of missiles make the rudder surfaces and lifting surfaces susceptible to faults. In practical scenarios, there is often a scarcity of fault data, and sometimes, it is even difficult to obtain such data. Currently, data-driven fault detection and localization methods heavily rely on fault data, posing challenges for their applicability. To address this issue, this paper proposes an HBOS (Histogram-Based Outlier Score) online fault-detection method based on statistical distribution. This method generates a fault-detection model by fitting the probability distribution of normal data and incorporates an adaptive threshold to achieve real-time fault detection. Furthermore, this paper abstracts the interrelationships between the missile’s flight states and the propagation mechanism of faults into a hierarchical directed graph model. By utilizing bilateral adaptive thresholds, it captures the first fault features of each sub-node and determines the fault propagation effectiveness of each layer node based on the compatibility path principle, thus establishing a fault inference and localization model. The results of semi-physical simulation experiments demonstrate that the proposed algorithm is independent of fault data and exhibits high real-time performance. In multiple sets of simulated tests with randomly parameterized deviations, the fault-detection accuracy exceeds 98% with a false-alarm rate of no more than 0.31%. The fault-localization algorithm achieves an accuracy rate of no less than 97.91%.