Addressing the real-time control challenges within large-scale, complex resource-constrained project scheduling, this paper investigates control strategies to ensure the on-time initiation of critical task nodes during the execution of aviation cluster mission plans in the presence of disturbances. Conventional resource-constrained project scheduling problem (RCPSP) models typically treat task start times as the primary decision variables, overlooking the intrinsic link between task duration and resource allocation. Moreover, their reliance on intelligent optimization algorithms struggles to simultaneously balance solution accuracy and computational efficiency, thus failing to meet the demands of precise, real-time control. This paper proposes a real-time project schedule control system with the primary objective of preventing delays in critical tasks. The system aims to maximize the remaining anti-disturbance capacity under resource constraints, and establishes five control constraints tailored to the practical problem’s characteristics. The limitations of traditional approaches mainly lie in the fact that they take the start time of each task as the decision variable. When the scale of task quantity in the project is large, the decision dimension increases exponentially; meanwhile, the start times of various tasks are interdependent, leading to extremely complex constraint relationships. To overcome the limitations of traditional methods, this paper introduces a precise control method based on the Critical Path Transform Tree (CPTT). This method takes task duration as the decision variable, calculates the start time of each task using a recursive formula, and integrates expert heuristic knowledge to transform the dynamic network schedule from a “black box” to a “gray box” model. It effectively addresses the technical challenge of reverse mapping in the recursive formula, ultimately realizing precise and real-time control of the project schedule. The simulation results show that while maintaining high solution accuracy, the computational efficiency of the proposed control method is significantly improved to 1.6 s—compared with an average of 6.9 s for the adaptive differential evolution algorithm—thus verifying its effectiveness and practicality in real-time control applications.