The Internet of Things defines a global and comprehensive network whose task is to monitor and control the physical world by collecting, processing, and analyzing data sensed by IoT devices. This network has succeeded in various areas, and one of its most important applications is in smart agriculture because there are many demands for producing high-quality foodstuff in the world. These demands need new production schemes in the agriculture area. In IoT, communication security is essential due to the extensive heterogeneity of IoT devices. In this paper, a cluster-tree-based secure routing approach using the dragonfly algorithm (CTSRD) is proposed for IoT. The proposed scheme presents a distributed and lightweight trust mechanism called weighted trust (W-Trust). W-Trust reduces the trust value corresponding to malicious nodes based on a penalty coefficient to isolate this node in the network. Furthermore, it improves the trust value of honest IoT devices based on a reward coefficient. Additionally, CTSRD introduces a trust-based clustering process called T-Clustering. In this clustering process, cluster head nodes (CHs) are selected among honest IoT nodes. Finally, CTSRD establishes a routing tree based on the dragonfly algorithm (DA) between CHs. This tree is called DA-Tree. To evaluate the quality of the routing tree, a new fitness function is provided in CTSRD. DA-Tree finds a secure, stable, and optimal routing tree to balance the consumed energy and boost the network lifetime. CTSRD is compared with EEMSR and E-BEENISH with regard to the network lifetime, consumed energy, and packet delivery rate. This comparison shows that our scheme can uniformly distribute the consumed energy in IoT and improves the energy consumption and network lifetime. However, it has a slightly lower packet delivery rate than EEMSR.