For scheduling in flexible manufacturing system (FMS), many factors should be considered, it is difficult to solve the scheduling problem by satisfying different criteria (production cost, utilization of system, number of movements of part, make-span, and tardiness in due date and so on) and constrains. The paper proposes mathematical model of a job shop scheduling problem (JSSP) to balance the load of all machines and utilize effectively all machines in FMS. This paper defines the evaluation function of the unbalance of the machine load and formulates the optimization problem with two objectives minimizing unbalance of the machine load and the total processing time, scheduling problem having been solved by integer linear programming, thus scheduling problem having been solved. The results of calculation show that the total processing time on all machines is reduced and machine loading is balanced better than previous works, and job shop scheduling also could be scheduled more easily in FMS.