Currently, Peer-to-Peer overlays can be classified into two main categories: unstructured and structured ones. Unstructured overlays are simple, robust, and powerful in keyword search. Structured ones can scale to very large systems in terms of node number and geography, and guarantee to locate an object within O(Log N) hops. However, both of them face difficulties in efficiency and security of overlays. For unstructured ones, the efficiency problem presented is poor scalability. For structured ones, it is long routing latency and enormous overhead on handling system churn. Moreover, both of them are vulnerable to malicious attacks. Peer-to-Peer overlays belong to application-level network. To a great extension, overlay network designs ignore physical characteristics. As the result, their structures are far from underlying physical network or the distribution pattern of overlay peers. These inconsistencies induce system common operations costly, such as routing and lookup. On the other hand, most peers are assumed to have uniform resources and similar behaviors. Thus, Peer-to-Peer protocols were designed to be symmetric. However, in the realistic environment, peers' resources and behaviors are highly skewed. Symmetric protocols actually compromise system performance. Frequently joining and leaving of peers generates enormous traffic. The significant fraction of peers with high latency/low bandwidth links increase lookup latency. Moreover, under the environment without mutual trust, Peer-to-Peer systems are very vulnerable for varied attacks because they lack a practical authentication mechanism. From a different perspective, this dissertation proposes to construct a highly efficient and secure Peer-to-Peer overlay based on the physical network structure of the Internet and network locality of overlay peers. By naturally integrating different network-aware techniques into the Peer-to-Peer overlay, a novel SNSA (Scalable Network Structure Aware) technique has been developed. It can provide accurate information of network locality of overlay peers and sufficient physical network structure of the Internet. Based on the valuable information, a unique Peer-to-Peer overlay, which can reflect network structure and locality of overlay peers, is constructed. Also, peers are assigned different roles by their resources and behaviors. Minor capable peers are involved in overlay core operations, such as routing and lookup. Major normal ones are organized into highly dependable teams, and assigned usual tasks, such as storing objects. Not only can this overlay support both structured and unstructured systems, but also the systems are highly efficient in routing and consuming much less bandwidth. As the observation that every peer must subject to the network configuration and administration imposed by ISPs, we propose to identify each peer by its physical network characteristic, net-print. Based on the SNSA technique and the net-print, a distributed authentication and secure routing mechanisms are developed under Peer-to-Peer environment. Beware of the fact that every overlay network maintains its own network proximity system. This dissertation proposes to build a common layer to provide such information for all overlays. By deeply analyzing requirements of current overlays, three kinds of primitives are designed to provide valued knowledge of physical network and overlay peers. Not only dose this method save network resource by eliminating duplicated probes, but it also provides an efficient way to share information between overlays.