Blockchain-based agricultural IoT systems face key challenges such as high delay and low transaction throughput. Existing complicated consensus mechanisms can cause IoT devices work inefficiently due to the limited computing, storage and energy resources. Additionally, many message exchanges can lead to high latency in the consensus process, which hinders the real-time applications of the agricultural IoT. Therefore, we propose Proof-of-Multifactor-Capacity (PoMC), an efficient and secure consensus mechanism for the agricultural IoT. It uses the communication capacity and credibility of a node as the evidence for making consensus. Moreover, a senator node lottery algorithm based on a credit mechanism and a new distributed incentive mechanism are designed to enhance security and motivate nodes to actively maintain the system. This paper analyses the performance of PoMC theoretically, including security, latency and system throughput, and presents a comparison of its asymptotic complexity with some existing consensus mechanisms. The simulation results demonstate that the average transaction validation latency and average consensus latency of PoMC have decreased by 10% and 23%. In addition, PoMC outperforms SENATE, PoQF and PBFT by 56%, 60% and 64% in terms of the system throughput, respectively.