Abstract: Seed cotton cleaning, a critical step in the cotton production and processing workflow, significantly influences the subsequent ginning process and the ultimate lint quality. The stripper and stick cleaner is an indispensable piece of machinery within the seed cotton cleaning process. Its primary function is to remove boll husks, thereby laying a solid foundation for the subsequent stages of cotton processing and ensuring the production of high-quality lint. In the working process, it relies mainly on centrifugal force created by the U-shaped saw cylinder and the stripping action of cleaning bars positioned around the saw cylinder to achieve separation of seed cotton and boll husks. Sea island cotton is the primary raw material for high-end textiles. Compared with upland cotton, the fibers of sea island cotton are softer, finer, and exhibit a higher coefficient of friction. Consequently, the existing stripper and stick cleaners designed specifically for upland cotton processing have issues such as low boll husk cleaning rate, high cotton loss rate, and significant fiber damage when cleaning machine-harvested sea island cotton. To address these issues, this study designed a stripper and stick cleaner for machine-harvested sea island cotton. Through an analysis of the fiber damage mechanism, the entire machine was determined to be a three-cylinder structure. Through an analysis of the physical and mechanical properties of machine-harvested sea island cotton, and combined with theoretical analysis of boll husk removal, the key structural parameters and operational parameter ranges of the boll husk removal device and doffing cylinder were designed. In November 2024, experiments were carried out at a cotton processing plant in the Aksu region of Xinjiang using machine-harvested long-staple cotton Xinhai 62 as the test sample. A single-factor experiment was carried out using the seed cotton feeding speed, U-shaped saw cylinder rotation speed, and U-shaped saw cylinder and cleaning bar spacing as the control factors, with the boll husk cleaning rate and cotton loss rate as the evaluation indices. The seed cotton feeding speed, U-shaped saw cylinder rotation speed, and U-shaped saw cylinder and cleaning bar spacing were determined to be in the ranges of 11-13 t/h, 170-238 r/min, and 13-19 mm, respectively. A three-factor quadratic regression orthogonal combination test protocol was developed using the Box-Behnken design method. The results were subjected to analysis of variance and response surface analysis using Design-Expert 13 software. The optimal working parameters obtained were: seed cotton feeding speed of 11.00 t/h, U-shaped saw cylinder rotation speed of 219.12 r/min, and U-shaped saw cylinder and cleaning bar spacing of 15.61 mm. The performance was predicted to have a boll husk cleaning rate of 64.85% and a cotton loss rate of 0.27%. The optimized parameters were rounded to the seed cotton feeding speed of 11.00 t/h, the U-shaped saw cylinder rotation speed of 220 r/min, and the U-shaped saw cylinder and cleaning bar spacing of 16 mm for the prototype test. Experimental verification showed that under the optimal working parameters, the average rate of boll husk cleaning was 64.23%, and the average cotton loss rate was 0.27%. Compared with the existing stripper and stick cleaner, the improved machine achieved a 6.54 percentage point increase in boll husk cleaning rate and a 0.81 percentage point reduction in cotton loss rate. Finally, through a fiber damage test, it was concluded that under optimal operating parameters, when processing machine-picked sea island cotton using the improved machine, the fiber length was reduced by 0.36 mm, and the fiber damage rate was 0.95%. In contrast, the existing stripper and stick cleaner reduced the fiber length by 1.02 mm and exhibited a 1.73 percentage point reduction in fiber damage rate. These findings can provide technical references for the development of a stripper and stick cleaner for machine-harvested sea island cotton.