This paper is concerned with the time-decay rates of the strong solutions of the three dimensional non-isentropic compressible magnetohydrodynamic (MHD) system. First, motivated by Pu–Guo’s result [Z. Angew. Math. Phys. 64 (2013) 519–538], we establish the existence result of a unique local-in-time strong solution for the MHD system. Then, we derive a priori estimates and use the continuity argument to obtain the global-in-time solution, where the initial data should be bounded in L1-norm and is small in H2-norm. Finally, based on Fourier theory and the idea of cancellation of a low-medium frequent part as in [Sci. China Math. 65 (2022) 1199–1228], we get the optimal time-decay rates (including highest-order derivatives) of strong solutions for non-isentropic MHD fluids. Our result is the first one concerning with the optimal decay estimates of the highest-order derivatives of the non-isentropic MHD system.