To improve the accuracy of dynamic analysis for flight vehicle airframe cabins with slot-nut type bolted flange joints, a modal vibration analysis method considering nonlinear stiffness of bolted flange joint is firstly proposed. An equivalent structural model is created to represent the bolted flange joint and cabin structure. Modal analysis is performed and the first three order bending frequencies are extracted. By using the orthogonal experimental method, the importance analysis of the design factors including connection thickness, stud number, and stud specifications is carried out. The results show that the proposed dynamic analysis method can well model the effect of slot-nut type bolted flange joint on flight vehicle airframe stiffness and normal vibration. The conncetion thickness of flange and the number of stud are critical design factors affecting cabin vibration frequency.