Cargo transfer vessels (CTVs) are designed to transfer cargo from a floating production storage and offloading (FPSO) unit into conventional tankers. The dynamic positioning system allows the CTV to maintain a safe position relative to the FPSO unit using a flexible cargo transmission pipe, and the CTV tows the tanker during operating conditions. The operation mode can be considered a synchronization tracking control problem. In this paper, a synchronization control strategy is presented based on the virtual leader–follower configuration and an adaptive backstepping control method. The position and heading of the following vessel are proven to be able to globally exponentially converge to the virtual ship by the contraction theorem. Then, the optimization problem of the desired thrust command from the controller is solved through an improved firefly algorithm, which fully considers the physical characteristics of the azimuth thruster and the thrust forbidden zone caused by hydrodynamic interference. To validate the effectiveness of the presented synchronous following strategy and thrust allocation algorithm, a scale model experiment is carried out under a sea state of 4 in a seakeeping basin. The experimental results show that the CTV can effectively maintain a safe distance of 100 m with a maximum deviation of 3.78 m and an average deviation of only 0.99 m in the wave heading 180°, which effectively verifies that the control strategy proposed in this paper can achieve safe and cooperative operation between the CTV and the FPSO unit. To verify the advantages of the SAF algorithm in the thrust allocation, the SQP algorithm and PSO algorithm are used to compare the experimental results. The SAF algorithm outperforms the SQP and PSO algorithms in longitudinal and lateral forces, with the R-squared (R2) values of 0.9996 (yaw moment), 0.9878 (sway force), and 0.9596 (surge force) for the actual thrusts and control commands in the wave heading 180°. The experimental results can provide technical support to improve the safe operation of CTVs.