Multi-layered networks have recently emerged as a new network model, which naturally finds itself in many high-impact application domains, ranging from critical inter-dependent infrastructure networks, biological systems, organization-level collaborations, to cross-platform e-commerce, etc. Cross-layer dependency, which describes the dependencies or the associations between nodes across different layers/networks, often plays a central role in many data mining tasks on such multi-layered networks. Yet, it remains a daunting task to accurately know the cross-layer dependency a prior. In this paper, we address the problem of inferring the missing crosslayer dependencies on multi-layered networks. The key idea behind our method is to view it as a collective collaborative filtering problem. By formulating the problem into a regularized optimization model, we propose an effective algorithm to find the local optima with linear complexity. Furthermore, we derive an online algorithm to accommodate newly arrived nodes, whose complexity is just linear wrt the size of the neighborhood of the new node. We perform extensive empirical evaluations to demonstrate the effectiveness and the efficiency of the proposed methods.