The ability to control the energy transfer in rare-earth ion-doped luminescent materials is very important for various related application areas such as color display, bio-labeling, and new light sources. Here, a phase-shaped femtosecond laser field is first proposed to control the transfer of multiphoton excited energy from Tm3+ to Yb3+ ions in co-doped glass ceramics. Tm3+ ions are first sensitized by femtosecond laser-induced multiphoton absorption, and then a highly efficient energy transfer occurs between the highly excited state Tm3+ sensitizers and the ground-state Yb3+ activators. The laser peak intensity and polarization dependences of the laser-induced luminescence intensities are shown to serve as proof of the multiphoton excited energy transfer pathway. The efficiency of the multiphoton excited energy transfer can be efficiently enhanced or completely suppressed by optimizing the spectral phase of the femtosecond laser with a feedback control strategy based on a genetic algorithm. A (1+2) resonance-mediated three-photon excitation model is presented to explain the experimental observations. This study provides a new way to induce and control the energy transfer in rare-earth ion-doped luminescent materials, and should have a positive contribution to the development of related applications.