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Field breeding trial-plot harvesting is one of the key processes in crop breeding, as any mixing between varieties during harvest directly leads to the invalidation of breeding data. Therefore, achieving zero-residue self-cleaning inside the machine during harvesting is essential. Existing studies have largely relied on simulations to optimize cleaning parameters. However, research specifically targeting the synergistic design of the mechanical and pneumatic components of the cleaning device to achieve efficient and thorough self-cleaning in complex real-world conditions remains lacking. To address this issue, this paper presents a novel cleaning system specifically designed for efficient self-cleaning and optimizes its key parameters. Key structural parameters of the straw walker, vibrating sieve, and cleaning fan were analyzed, establishing preliminary ranges for crank speed, sieve-airflow angle, and fan speed. A test bench was developed, and single-factor experiments were conducted to investigate the effects of these parameters on core self-cleaning indicators, including the self-cleaning rate and self-cleaning time. The optimal parameter combination was obtained using the Box–Behnken design (BBD) response surface methodology: a crank speed of 390.80 r/min, a sieve-airflow angle of 29.88°, and a fan speed of 1995 r/min. Bench tests validated that the system achieved excellent cleaning performance while ensuring a self-cleaning rate of 100% and a reduced self-cleaning time of 20 s. The system’s effectiveness was further validated through field experiments using a 4LX1 prototype harvester on three wheat varieties. Results demonstrated zero grain mixing between plots, with self-cleaning times of 9–12 s. Both bench and field test results exceeded the relevant standards, effectively resolving the long-standing issue of grain residue in trial plot harvesting. Through dual validation, this study provides a referential solution for addressing grain residue and establishes a theoretical foundation for the synergistic design of efficient and precision breeding harvest technologies.