Massive smart water conservancy object (WCO) need to be connected for real-time monitoring and control, which produces massive data. Unfortunately, heterogeneous data structures and semantics lead to low interoperability between WCO and management systems. To address this challenge, we propose a novel interoperability structure for a smart water conservancy system based on the Internet of Things (IoT), and the key design includes a smart WCO terminal, interoperability network, special interoperability protocol, WCO information model, and cloud platform. Universal terminal and network are the base of interoperability hardware, and special interoperability protocol and information model for interconnection of WCO are designed for smart water conservancy management system. WCO can be connected to a water conservancy Big Data processing cloud platform for interoperability applications. The application results demonstrate that our proposed WCO’s interoperability structure has obvious advantages than the general IoT at WCO interoperability. The interoperability protocol is reliable, the information model can ease interoperability and security, and the semantic dictionary is very rich and covers all semantic services of WCO.