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The influence of GaAs substrate on the transmission performance of a multi-film Fabry-Peerot filter (FPF), fabricated by metalorganic chemical vapor deposition epitaxial growth on GaAs substrate, is investigated using the transfer matrix method. On the basis of the theoretical simulation, we determine that the quality of the resonant transmission peak of this epitaxially grown FPF (EG-FPF) deteriorates through splitting when the substrate is taken into account. Rapid periodic oscillation of peak-transmittivity along with the alteration of substrate thickness is also observed in the simulation results. Finally, a remarkably improved transmission performance of the EG-FPF is obtained by thinning the substrate down to a suitable thickness range through well-controlled grinding and polishing.