Time synchronization is critical for wireless sensors networks in industrial automation, e.g., event detection and process control of industrial plants and equipment need a common time reference. However, cyber-physical attacks are enormous threats causing synchronization protocols to fail. This paper studies the algorithm design and analysis in secure time synchronization for resource-constrained industrial wireless sensor networks under Sybil attacks, which cannot be well addressed by existing methods. A node-identification-based secure time synchronization (NiSTS) protocol is proposed. The main idea of this protocol is to utilize the timestamp correlation among different nodes and the uniqueness of a node’s clock skew to detect invalid information rather than isolating suspicious nodes. In the detection process, each node takes the relative skew with respect to its public neighbor as the basis to determine whether the information is reliable and to filter invalid information. The information filtering mechanism renders NiSTS resistant to Sybil attacks and message manipulation attacks. As a completely distributed protocol, NiSTS is not sensitive to the number of Sybil attackers. Extensive simulations were conducted to demonstrate the efficiency of NiSTS and compare it with existing protocols.