The powered parafoil system is obtained by adding the propeller thrust to the unpowered parafoil system, and has coupling and nonlinear characteristics, which make its precise control more difficult than that of the unpowered parafoil system. To achieve the trajectory tracking control of the powered parafoil system in the field of precision airdrop, a mathematical model of the 6-DOF of the powered parafoil system is established first. Then, a new trajectory tracking strategy is proposed, which can overcome the limitations of the traditional guidance-based trajectory tracking strategy. We design lateral, longitudinal, and velocity controllers on the basis of the motion characteristics of the powered parafoil system. Then, we adopt the widely used PID control strategy in engineering. In response to the difficult of the PID controller parameter tuning of the powered parafoil system, we achieve the PID controller parameter tuning with the ecosystem particle swarm optimization (ESPSO) of the swarm intelligence optimization algorithm. The effectiveness of the algorithm is verified by simulation experiments. Results show that the proposed algorithm can obtain high trajectory tracking accuracy even when a deviation in the initial state and a random gust wind disturbance in the outside world occur regardless of the method of the multiphase homing or the optimal control homing adopted. The proposed trajectory tracking strategy also has strong robustness and adaptability.