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In this study, the dynamic response of FGM (Functionally graded materials) micro-cantilever immersed in fluids under high-frequency photothermal excitation was investigated theoretically. The temperature along the length of microcantilever can be obtained analytically by using Fourier heat conduction theory. The axial thermal stress varying along the thickness can be obtained by the temperature distribution. Using concept of physical neutral surface and thermal stress, photothermal driving force was obtained analytically by using thermoelastic theory. The hydrodynamic force was presented by means of Sader’s method. Based on the Euler-Bernoulli beam model, effective bending modulus and effective density of the FGM cantilever, dynamical deflection fields in fluids can be obtained analytically by using mode superposition method. Theoretical analysis showed that the influence of volume fraction in vacuum or air is more significant than in fluids, and the volume fraction has a less influence when the dimension of microcantilever get smaller. This study can be valuable to users and designers of FG microcantilever-based structures in MEMS/NEMS.