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The paper studies multi-layer optimization in service oriented cloud computing to optimize the utility function of cloud computing, subject to resource constraints of an IaaS provider at the resource layer, service provisioning constraints of a SaaS provider at the service layer, and user QoS (quality of service) constraints of cloud users at application layer, respectively. The multi-layer optimization problem can be decomposed into three subproblems: cloud computing resource allocation problem, SaaS service provisioning problem, and user QoS maximization problem. The proposed algorithm decomposes the global optimization problem of cloud computing into three sub-problems via an iterative algorithm. The experiments are conducted to test the efficiency of the proposed algorithm with varying environmental parameters. The experiments also compare the performance of the proposed approach with other related work.