Supported noble metal nanoparticles (NPs) are widely applied as heterogeneous catalysts in numerous reactions, in which the morphology of metal clusters is of crucial to the catalytic performance. In this study, the multiscale simulations concerned with the adsorption and morphological behavior of Pd, Au clusters and NPs on Mo2C, Mo2CO2 and Mo2CF2 have been performed systematically by density functional theory (DFT) and molecular dynamics (MD). There is an obvious morphological tendency of two-dimension (2D) to three-dimension (3D) for supported Pd-n/Au-n (n= 4-6) clusters from bare to O, F-terminated Mo2C. The electronic properties analysis shows that more charge transfer occurred on clusters leads to the stronger interaction between clusters and Mo2C MXene. The plots of projected density of states (PDOS) describe that the O, F groups weaken the strong interaction between clusters and bare Mo2C, showing that the nature of the change of morphology is the modification of d states of Pd, Au NPs by the introduction of O, F groups. The MD simulations of large supported Pd-n/Au-n NPs on bare and functionalized Mo2C are corresponded to the 2D-3D growth of DFT result, which shows that for metal NPs, the average coordination number as well as the interaction of Pd/Au NPs and support varies with the order of bare-O-F. Based on the multiscale simulations, the morphology ranges from Pd/Au clusters to NPs have been governed efficiently by surface groups, which may enlighten the design of metal-supported catalysts.