Double layer ACO algorithm for the multi-objective FJSSP Scheduling for the flexible job shop is very important in both fields of production management and combinatorial optimization. In this work, a double layer Ant Colony Optimization (ACO) algorithm is proposed for the Flexible Job Shop Scheduling Problem (FJSSP). In the proposed algorithm, two different ACO algorithms are applied to solve the FJSSP with a hierarchical way. The primary mission of upper layer ACO algorithm is achieving an excellent assignment of operations to machines. The leading task of lower layer ACO algorithm is obtaining the optimal sequencing of operations on each machine. Experimental results suggest that the proposed algorithm is a feasible and effective approach for the multi-objective FJSSP.