Material surfaces may have a remarkable effect on the mechanical behavior of magneto-electro-elastic (or multiferroic) structures at nanoscale. In this paper, a surface magneto-electro-elasticity theory (or effective boundary condition formulation), which governs the motion of the material surface of magneto-electro-elastic nanoplates, is established by employing the state-space formalism. The properties of anti-plane shear (SH) waves propagating in a transversely isotropic magneto-electro-elastic plate with nanothickness are investigated by taking surface effects into account. The size-dependent dispersion relations of both antisymmetric and symmetric SH waves are presented. The thickness-shear frequencies and the asymptotic characteristics of the dispersion relations considering surface effects are determined analytically as well. Numerical results show that surface effects play a very pronounced role in elastic wave propagation in magneto-electro-elastic nanoplates, and the dispersion properties depend strongly on the chosen surface material parameters of magneto-electro-elastic nanoplates. As a consequence, it is possible to modulate the waves in magneto-electro-elastic nanoplates through surface engineering.