Abstract: To develop a larger in-line plasma enhanced chemical vapor deposition (PECVD) device, the length of the linear microwave plasma source needs to be increased to 1550 mm. This paper proposes a solution to the problem of plasma inhomogeneity caused by increasing device length. Based on the COMSOL Multiphysics, a multi-physics field coupling model for in-line PECVD device is developed and validated. The effects of microwave power, chamber pressure, and magnetic flux density on the plasma distribution are investigated, respectively, and their corresponding optimized values are obtained. This paper also presents a new strategy to optimize the wafer position to achieve the balance between deposition rate and film quality. Numerical results have indicated that increasing microwave power and magnetic flux density or decreasing chamber pressure all play positive roles in improving plasma homogeneity, and among them, the microwave power is the most decisive influencing factor. It is found that the plasma homogeneity is optimal under the condition of microwave power at 2000 W, chamber pressure at 15 Pa, and magnetic field strength at 45 mT. The relative deviation is within −3.7% to 3.9%, which fully satisfies the process requirements of the equipment. The best position for the wafer is 88 mm from the copper antenna. The results are very valuable for improving the quality of the in-line PECVD device.