With the globe warming, heat stress (HS) has frequently affected animal production. Selenium (Se) is an essential trace element for animals and exerts most of its biological functions through selenoproteins. We previously demonstrated that the damage to C2C12 cells by HS accompanied with the response of selenoprotein encoding genes and proteins. The objective of this study was to investigate whether selenium supplementation (sodium selenite, SS and selenomethionine, SeMet) could alleviate the negative effect of heat stress on the differentiation of C2C12 cells, and interpret the potential corresponding selenoproteins response. The differentiated cells were cultured for 4 and 8 days under different condition: at 37 °C, 41.5 °C and 41.5 °C with 0.5 μmol Se/L SS or SeMet, and the HSP70, cell apoptosis, selenoproteins and cell differentiation-related gene or protein were detected. The result showed that HS up-regulated (P < 0.05) mRNA and protein levels of HSP70 and gene expression of AMPKα1 and AMPKα2, and down-regulated (P < 0.05) mRNA or protein levels of MYOGENIN and MYOD. Meanwhile, up to 15 and 17 selenoprotein genes expression were significantly changed response to 4-and 8-days HS challenge, respectively. Relative to the HS group, SS and SeMet supplementation down-regulated the mRNA and protein abundance of HSP70 to different degrees, and partly recovered (P < 0.05) the mRNA or protein abundance of MYOGENIN and MYOD at 4th and 8th day. Especially, 16 and 10 selenoprotein genes expression in cells affected by HS were altered by SS and SeMet supplementation, respectively. Both SS and SeMet supplementation modestly increased (P < 0.05) protein levels of GPX1 and SELENON in cells under HS. In summary, Se supplementation partly alleviated the negative impact of HS on myogenic differentiation of C2C12 cells and the process may associate with the alternation of selenoprotein expression pattern, and SeMet exhibits better effect than SS.