In this paper we first introduce fractional orthogonal Jacobi functions then we obtain a new fractional derivative operational matrix for these orthogonal functions. It is based on the relationship between the coefficients of the fractional Taylor series and fractional Jacobi function expansions. We also apply this new operational matrix to the collocation method for solving general multi-order fractional differential equations (FDEs) and nonlinear fractional integro–differential equations (FIDEs). We also present several test problems. The numerical results show that our new scheme is very effective and convenient for solving FDEs and FIDEs.