Urban rail transit, as a main mode of travel, has always been concerned with the balanced relationship between energy consumption and transport efficiency. The advent of the virtually coupled train set (VCTS) has significantly enhanced the efficiency of existing railway lines. Both energy consumption and comfort during the operation of VCTS control technology have emerged as significant challenges for the development of VCTS since the inception of onsite testing. A review of the current research status of VCTS control systems has revealed that the majority of current formation control systems are focused on the safe operation of formation trains, the stability of train control systems, and safe train separation models. However, a case study has shown there is a strong correlation between train operating intervals, train control strategies, and train operating energy consumption. Therefore, it is necessary to design and plan the operation modes of formation trains for different train operation requirements. This paper presents four distinct control modes, developed through the integration of the most prevalent VCTS control strategies, operational modes, and operational requirements. The design of these control modes is guided by considerations of energy consumption, safety, and comfort during train operation. A case study of Beijing Subway Line 11 revealed a significant correlation between energy consumption, control mode, and safety under different control modes. In particular, the correlation between train running intervals and energy consumption in a high-precision tracking state provides valuable technical support for the future operation of VCTS technology in different periods, scenarios, and environments.