Interoperability testing and analysis tools provide a means for achieving and assuring the integrity of multivendor intelligent electronic devices (IEDs) data exchanges. However, the testing and analysis are very time consuming and error prone, and these problems worsen when a substation becomes large and complex during the engineering process, commission, replacement, maintenance, and extension. To address this challenge, this paper presents a virtual digital substation test system (VDSTS) with interoperability analysis tools for assessing and identifying the engineering challenges for the multiple-vendors digital substation. This VDSTS consists of three parts: (i) A virtual digital substation modelling for generating real-time digital substation primary plant operation and fault conditions, (ii) a standard IEC 61850-based substation protection, automation, and control (PAC) system architecture with multivendor IEDs and bay solutions, and (iii) multivendor Substation Configuration description Language (SCL) tools and in-house built data visualisation tool. The study focuses on the interoperability testing of sampled values (SV), generic object-oriented substation events (GOOSE), and manufacturing message specification (MMS) communication services, as defined in IEC 61850. The main issues identified are compatibility issues of SCL tools, protocol implementation issues, different information models, and application limitations. The outcomes will help utilities to reduce the risks associated with the general rollout of digital substations.