The quantum-inspired evolutionary algorithm (QEA) uses several quantum computing principles to optimize problems on a classical computer. QEA possesses a number of quantum individuals, which are all probability vectors. They work well for linear problems but fail on problems with strong interactions among variables. Moreover, many optimization problems have multiple global optima. And because of the genetic drift, these problems are difficult for evolutionary algorithms to find all global optima. Local and global migration that QEA uses to synchronize different individuals prevent QEA from finding multiple optima. To overcome these difficulties, we proposed a quantum-inspired evolutionary algorithm with linkage learning (QEALL). QEALL uses a modified concept-guide operator based on low order statistics to learn linkage. We also replaced the migration procedure by a niching technology to prevent genetic drift, accordingly to find all global optima and to expedite convergence speed. The performance of QEALL was tested on a number of benchmarks including both unimodal and multimodal problems. Empirical evaluation suggests that the proposed algorithm is effective and efficient.