This paper is devoted to studying difference indices of quasi-prime difference algebraic systems. We define the quasi dimension polynomial of a quasi-prime difference algebraic system. Based on this, we give the definition of the difference index of a quasi-prime difference algebraic system through a family of pseudo-Jacobian matrices. Some properties of difference indices are proved. In particular, an upper bound of difference indices is given. As applications, an upper bound of the Hilbert-Levin regularity and an upper bound of orders for the difference ideal membership problem of a quasi-prime system are deduced.