In order to analyze the effects of stiffeners’ cross section shape on the vibration fatigue property of stiffened panels, two kinds of panels were carried out. Firstly, the stiffened panels with L-shaped stiffener and T-shaped stiffener were excited by base motion at the resonance frequency. The effects of different stiffeners’ shape on the frequency and vibration fatigue life of thin-walled structures were studied experimentally. The possible mechanism was analyzed theoretically and the test process was validated by MSC software. Secondly, based on the reasonable FEM simulation, the thin-walled stiffened panels were excited by a sinusoidal distributed load under two boundary conditions (clamped and simply supported) in MSC simulation. The effects of stiffeners with six shapes were discussed on the frequency, stress distribution and vibration fatigue life of thin walled structures. The results showed that the first natural frequency of panel with Z-shaped stiffener is the maximum among all the configurations. And the peak value of the stress occurred at the same position. When the edges of the panel are fully clamped, the damage position occurred at the side of the stiffener and the fatigue life of Z-shaped stiffened panels is the longest. When the edges of the panels are simply clamped, the damage position occurred at the centre region of the panels and the L-shaped stiffened panels had the longest life.