The Noether symmetry, the Mei symmetry and the conserved quantities of discrete holonomic system in phase space are studied in this paper. Using the difference discrete variational approach, the difference discrete variational principle of discrete holonomic system in phase space is derived. The discrete canonical equations and energy evolution equation are established. The criterion of Noether symmetry and Mei symmetry of the system are given. The discrete Noether and Mei conserved quantities and the conditions for their existence are obtained. An example is discussed to show the applications of the results.