A Wireless Power Transfer (WPT) system, known for its contactless power delivery, is extensively used for power supply in spacecraft applications. Achieving efficient and stable power transfer necessitates the integration of DC/DC converters on both the primary and secondary sides of WPT systems for power conversion and control. Traditional efficiency optimization methods primarily focus on impedance matching within the wireless power resonance network, often neglecting the overall efficiency optimization of multi-stage DC-DC and WPT systems. This oversight results in suboptimal overall system efficiency despite optimal efficiency in the wireless transmission segment. Additionally, the time-varying nature of mutual inductance and load parameters during power transmission in WPT systems presents challenges for maximum efficiency tracking and power control. This paper introduces a multi-level coordinated control efficiency optimization method for WPT systems utilizing the particle swarm optimization (PSO) algorithm. This method takes into account the transmission losses across all power conversion units within the WPT system, establishing a mathematical model for the joint optimization of overall system transmission efficiency and power. The PSO algorithm is then employed to solve this optimization model using estimated mutual inductance and load values. By adjusting the DC/DC converters on both sides, the method ensures optimal overall system efficiency and consistent power transmission. Experimental results indicate that under varying load and mutual inductance conditions, a Series–Series (SS) compensated WPT system using this method achieves a 200 W power output with maximum efficiency tracking, a power output error of 0.63%, and an average transmission efficiency of 86.2%. This demonstrates superior power transmission stability and higher efficiency compared to traditional impedance matching methods.