Analysis was started with character of fatigue failure and damage evolution of structure. The structure reliability analysis model which expressed in fatigue damage of critical parts was given. The damage and reliability evaluation technique and corresponding parameter index of fatigue critical parts of in service aircraft were presented by basing on above model. The method based on integrated data of full-scale fatigue test on aircraft structure at room environment and flight parameters of every aircraft recorded in service. The method can carry out timely calculating structure damage state and reliability using flight parameters of every aircraft, and can satisfy with requirement of fatigue damage monitoring technique of aircraft in service. Finally the engineering demonstration based on usage of certain type aircraft was given. The method can be applied to timely evaluating structure damage and reliability of certain type aircraft, as also can provide important service information of every aircraft structure in service for the user. Then it is possible to allocating and using every aircraft in service reasonable with the precondition of ensuring aircraft structure safely.