A linkage mechanism with an elliptical motion trajectory includes a main body having two guiding tracks with a changeable lifting angle, a flywheel assembly and two handles installed on a front side of the main body, a first linkage rod pivotally attached between guiding rods of two driving linkage assemblies and two cranks of the flywheel assembly. The two pedals respectively include a front end pivotally attached onto each one of the cranks. Each one of the pedals moves together each one of the guiding rods and along each one of the guiding tracks and drives the flywheel assembly and each one of the handles to move forward and backward.