Visual, motion control, and programmable logic controller (PLC) systems are becoming increasingly inseparable and important in manufacturing. However, the types of programs and hardware used in these systems are numerous, and there are many communication protocols and mixed development methods among the systems; meanwhile, the requirements and complexities of these systems are ever growing. All these factors hinder application implementation for users, and very few reported studies have researched the integration of these three systems to ease complexity. Most of these studies have focused on individual applications. In this paper, we propose a multilevel flexible architecture based on a vision control algorithm (VCA) protocol. This multilevel architecture includes a flexible layer, a control layer, and an algorithm layer. The flexible layer is used to seamlessly integrate the visual system and the embedded PLC (ePLC). The VCA protocol is designed for data interactions between the layers. Correspondingly, customized hardware, memory allocation, and Petri-net-based multithreading structure of the proposed architecture are described in detail. Then, two cases are implemented: a winding machine with a visual system that obtains a regular winding effect by correcting $\theta$ , and a binocular catching robot uses cameras to track the trajectory and successfully catch a ball by adjusting speed and position. The results indicate that the proposed VCA-based architecture could easily be applied to two very different scenarios.