Abstract: IEEE802.15.4e is the latest MAC layer standards for the industrial Internet of things, which enables highly reliable and ultra-low power wireless networking through time synchronization technique. In cyberspace where an adversary may attack the networks through various ways, time synchronization becomes an attractive target due to its importance. If an adversary launches time synchronization attack, it will paralyze the whole network communication, the node localization and data fusion application. However, the time synchronization protocol is not insufficient to be protected in IEEE802.15.4e standard. So it is crucial to design a secure time synchronization protocol. First, we develop a secure single-hop ASN synchronization and a secure single-hop device-to-device synchronization using hardware-assisted encryption and authentication. And we also adopt the 2s+1 method and threshold filter algorithm. Second, we develop a secure multi-hop time synchronization mechanism which adopts a rank-based intrusion detection algorithm. Third, theoretical analysis and experiments show that the proposed countermeasures can successfully defend against external attacks and insider attacks, as well as high clock accurate and low power consumption.