The invention discloses a fatigue system reliability analysis method of a composite material laminated structure. According to the method, under the action of a fatigue load and a given constraint condition, multiple failure modes of the structure and correlation of the failure modes are fully considered, so that system reliability analysis is carried out. The method comprises the following steps:firstly, calculating the failure probability of each failure element in different failure modes by combining a two-dimensional Hashin criterion according to specific characteristics of laminated plate structure materials, loads and the like, and considering that a layer with the maximum failure probability is damaged; secondly, according to the built one-way laminated plate degradation model, degrading material attributes in the fatigue loading process, subjecting the degraded model to reanalysis, calculating the failure probability of each failure element, and determining a main failure path; and finally, checking the residual strength of the structure after cyclic loading is finished, establishing a fatigue system reliability index on the basis, and providing guidance and reference forsubsequent analysis and optimization.