The advancement of new generation information technology has made autonomous transportation systems (ATS) a cutting-edge research direction. Within this field, interoperability technology, which can facilitate collaborative operations across heterogeneous transportation entities, serves as the critical enabler for transitioning from human-centric control to highly autonomous operations. However, current research faces fundamental challenges such as conceptual ambiguity, unclear hierarchical taxonomy, and insufficient core technological maturation. To address these problems, this study provides a comprehensive and systematic explanation of interoperability technology. First, a unified definition of ATS interoperability is established, and a three-layer framework is proposed: (1) information interoperability, (2) function interoperability, and (3) element interoperability. Subsequently, the corresponding scientific issues and research progress at each level are analyzed. Finally, we point out key application challenges and future research directions. This work aims to provide fundamental references for breakthroughs in ATS interoperability technology development and validation.