The SiTian Project represents a groundbreaking initiative in astronomy, aiming to deploy a global network of telescopes, each with a 1 m aperture, for comprehensive time-domain sky surveys. The network's innovative architecture features multiple observational nodes, each comprising three strategically aligned telescopes equipped with filters. This design enables three-color (g, r, i) channel imaging within each node, facilitating precise and coordinated observations. As a pathfinder to the full-scale project, the Mini-SiTian Project serves as the scientific and technological validation platform, utilizing three 30 cm aperture telescopes to validate the methodologies and technologies planned for the broader SiTian network. This paper focuses on the development and implementation of the Master Control System (MCS), and the central command hub for the Mini-SiTian Array. The MCS is designed to facilitate seamless communication with the SiTian Brain, the project's central processing and decision-making unit, while ensuring accurate task allocation, real-time status monitoring, and optimized observational workflows. The system adopts a robust architecture that separates front-end and back-end functionalities. A key innovation of the MCS is its ability to dynamically adjust observation plans in response to transient source alerts, enabling rapid and coordinated scans of target sky regions. The paper provides an in-depth analysis of the system's internal components, including the communication system, which is critical for seamless network operation. Extensive testing has validated the functionality, reliability, and compatibility of these components within the overall system architecture. The successful deployment of the MCS in managing the Mini-SiTian Array has demonstrated its practicality and efficacy in collaborative observation and distributed control. By simplifying cluster management and ensuring data integrity, the MCS represents a significant advancement in astronomical observation control systems. Its scalable and adaptable design not only supports the future expansion of the SiTian network but also provides a blueprint for other large-scale telescope arrays, marking a transformative step forward in time-domain astronomy.