Differential evolution (DE) is an effective and efficient evolutionary algorithm in continuous space. The setting of control parameters is highly relevant with the convergence efficiency, and varies with different optimization problems even at different stages of evolution. Self-adapting control parameters for finding global optima is a long-term target in evolutionary field. This paper proposes a two-layered DE (TLDE) with self-adaptive control parameters combined with niching method based mutation strategy. The TLDE consists of two DE layers: A bottom DE layer for the basic evolution procedure, and a top DE layer for control parameter adaptation. Both layers follow the procedure of DE. Moreover, to mitigate the common phenomenon of premature convergence in DE, a clearing niching method is brought out in finding efficient mutation individuals to maintain diversity during the evolution and stabilize the evolution system. The performance is validated by a comprehensive set of twenty benchmark functions in parameter optimization and competitive results are presented.