In order to carry out the fatigue and damage tolerance analysis of the joint connecting fuselage and landing gear structure, a kind of rod element with very small stiffness is laid on the edge of stiffener and cut-outs when the detail finite element model of main joint is built. By using this method, the stress distribution of many different load cases can be obtained. Next spectrum of the special rod elements are edited and rain-flow counting is carried out. The load case which the maximum stress is related to is obtained, a method of obtaining fatigue weak case and fatigue weak sites is proposed. On this basis, DFR method is used to carry out the fatigue analysis, and Nasgro equation is adopted to carry out the damage tolerance analysis. The process can provide the theoretical instruction for fatigue strength assessment of other complex joint structure.