Abstract—The emerging paradigm of Software Defined Network (SDN) and virtualization technology promises an efficient solution for network providers to deploy services. Adopting them not only facilitates network management but also helps reduce the cost of maintaining network infrastructure. However, despite these advantages, there are still obstacles that must be overcome before SDN and virtualization can advance to reality in industrial deployments. In this paper, we focus on two well-researched issues, namely controller-switch assignment and Virtual Network Function (VNF) placement. Unlike prior works, our purpose is to jointly solve these two problems, accounting for the complex and counter-intuitive manner they are related to each other. We present a service chain aware framework (SACO) that enables the controllerswitch association in a multi-controller network regarding the relationship of switches via their connected VNFs that implement service components of the chain. We also propose a model and formulate the joint optimization problem of dynamic controllerswitch mapping and VNF allocation. We apply the Lyapunov optimization framework to transform a long-term optimization problem into a series of real-time problem and employ the Markov approximation method to find a near-optimal solution. Simulation results show that our service chain aware approach improves the system cost up to 10 ∼ 43% compared to the state-of-the-art solutions.