To find out preferred fault is of great importance for evaluation of regional stability and site selection. Herein, a novel model was presented to evaluate preferred fault based on rough set and set pair theory. Firstly, evaluation indexes were selected by means of the preferred plane theory. Then attribute reduction was conducted for evaluation samples, and objective weights were specified according to attribute importance of the reduced indexes. Moreover, the set pairs between evaluation samples and optimum or inferior indexes were constructed to analyze identical degree, contrary degree and set pair potential, and assessment model for preferred fault was also described. The results from the practical example show that dimension preferred index (LPI), distance preferred index (DPI) and time preferred index (TPI) have great influences on fault activity, and Maoshan fault, Tanlu fault and Yangtze river fault are preferred faults. Comparisons of these results from practical example with other methods show that this proposed method used to find out preferred fault is feasible and effective, and more objective.