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Rayleigh-Taylor (RT) instability occurs in a variety of scenario as a consequence of fluids of different densities pushing against the density gradient. For example, it is expected to occur in the ion acceleration of solid density targets driven by high intensity lasers and is crucial for the acceleration process. Yet, it is essential to understand the dynamics of the RT instability, a typical way to measure this phenomenon requires sophisticated diagnostics such as streak X ray radiography. Here, we report on experimental observation on periodic modulation in the energy spectrum of laser accelerated proton beams. Interestingly, theoretical model and two-dimensional particle-in-cell simulations, in good agreement with the experimental finding, indicated that such modulation is associated with periodic modulated electron density induced by transverse Rayleigh-Taylor-like instability. Furthermore, the correlation between the RT instability and the ion acceleration provides an interpretation to trace the development of the RT instability from the modulated proton spectrum. Our results thus suggest a possible tool to diagnose the evolution of the RT instability, and may have implications for further understanding for the accelerating mechanisms as well as optimization strategies for laser driven ion acceleration.