With the mobile communication system evolving into 6th-generation (6G), the Internet of Everything (IoE) is becoming reality, which connects human, big data and intelligent machines to support the intelligent decision making, reconfiguring the traditional industries and human life. The applications of IoE require not only pure communication capability, but also high-accuracy and large-scale sensing capability. With the emerging integrated sensing and communication (ISAC) technique, exploiting the mobile communication system with multi-domain resources, multiple network elements, and large-scale infrastructures to realize cooperative sensing is a crucial approach to satisfy the requirements of high-accuracy and large-scale sensing in IoE. In this article, the deep cooperation in ISAC system including three perspectives is investigated. In the microscopic perspective, namely, within a single node, the cooperation at the resource-level is performed to improve sensing accuracy by fusing the sensing information carried in the time-frequency-space-code multi-domain resources. In the mesoscopic perspective, the sensing accuracy could be improved through the cooperation of multiple nodes including Base Station (BS), User Equipment (UE), and Reconfigurable Intelligence Surface (RIS), etc. In the macroscopic perspective, the massive number of infrastructures from the same operator or different operators could perform cooperative sensing to extend the sensing coverage and improve the sensing continuity. This article may provide a deep and comprehensive view on the cooperative sensing in ISAC system to enhance the performance of sensing, supporting the applications of IoE.