The invention discloses a fatigue stress spectrum analysis method and system of a longitudinally connected ballastless track on a bridge for improving the simulation accuracy of the fatigue stress spectrum of the longitudinally connected ballastless track on the bridge during service and providing important support for the fatigue design of the longitudinally connected ballastless track on the bridge. The method comprises the following steps: independently establishing a longitudinally connected ballastless track-bridge temperature field calculation model, a high speed train-longitudinally connected ballastless track-bridge three-dimensional finite element coupling dynamics model and a longitudinally connected ballastless track-bridge-bridge abutment longitudinal interaction model; utilizing the models to research the stress time travel curve and the fatigue stress spectrum of the longitudinally connected ballastless track on the bridge during the service under the composite actions of loads including a train vertical load, a train longitudinal load, a ballastless track concrete temperature load, a ballastless track concrete temperature gradient load, a ballastless track concrete contraction load, a ballastless track prestress load and the like. The mechanical model of the invention is finer, and a load model is more perfect.