The need of manufacturing industries to adapt to the demand from customers and the volatile market drives the need for digitalization to realize the so-called smart factory. Smart factory, Compared to traditional factories, smart factory needs to possess high flexibility and stability and often has to employ digital twin. Compared to IEC 61131-3 standard used in traditional industrial production, IEC 61499 standard can bring more advantages to meet the realization of Smart Factory, such as flexibility, distribution and event-driven execution. In this paper, we propose a new Virtual Commissioning (VC) architecture for IEC 61499-based control applications. We build an online collaborative VC platform with the help of cloud computing and containerization technologies. Furthermore, we discuss and propose the utilization of soft-PLC containers from different vendors to meet users’ commissioning requirements for different hardware configurations. Compared with the traditional offline single-person debugging method, our proposed architecture can improve the flexibility, collaboration and efficiency of control software debugging in a more interactive and collaborative style via the online platform we implemented.