Abstract: Efficient cleaning equipment is often needed in the post-harvesting of Camellia oleifera fruits. Existing devices are limited to suboptimal separation and structural complexity. In this study, a drum-felt cleaning machine was developed to integrate an upper and lower drum mechanism, felt rings, and a throwing plate in a coordinated manner. Effective separation of shell and seed mixtures was then achieved in the machine. The cleaning performance of the machine was systematically evaluated via single-factor and multi-factor orthogonal experiments. Two response indicators were improved, including the seed content in the shell and the shell content in the seed. Four independent variables were investigated, including rotational speed of the drum, feeding angle, moisture content of the shell material, and cumulative cleaning quantity. A single-factor experiment revealed that the increasing drum speed reduced the shell rate within seeds, but there was an increase in the seed rate within shells. The shell content in the seed initially decreased and then increased as the feeding angle increased. While the seed content in the shell rose consistently. A decreasing moisture content of the shell material caused a sharp decline in the shell content in the seed, while the seed content increased in the shell. The individual parameters on separation were used to select the factor ranges for later optimization. A multi-factor orthogonal experiment was designed for the best combination of parameters. The cleaning performance was most significantly dominated by the interaction among drum speed, feeding angle, and moisture content. The best combination of parameters was found as a drum speed of 15.00 r/min, a feeding angle of 3.5°, and a shell moisture content of 27.00%. The better performance of the machine was achieved with a shell content in the seed of 3.51% and a seed content in the shell of 3.49%. These experimental values closely matched the simulated best values from the multi-factor optimization model, thereby confirming the reliability and accuracy of the experimental design and the optimization. The structural design of the cleaning machine proved to be effective. Dual drums and felt bonding were used to manage Camellia oleifera fruit shell-seed mixtures. Dual-drum configuration enhanced the material interaction surface and separation efficiency, while the felt elements contributed to gentle handling and reduced mechanical damage to the seeds. The throwing plate also helped material flow and distribution, showing consistent feeding and uniform processing. Moisture content is also highlighted during separation. Excessive moisture tended to cause agglomeration and adhesion, thus impairing separation efficiency, whereas overly dry material increased dust and fine particles. The feeding angle was found to influence the residence time and movement trajectory of the material within the cleaning zone, thereby affecting separation accuracy. Drum speed directly impacted the centrifugal force and agitation intensity, particularly for dislodging shells from seeds. The high stability of cumulative cleaning quantity was obtained under continuous operation, particularly for practical application in commercial settings. Overall, the drum-felt cleaning machine improved the efficiency and quality of camellia oleifera fruit processing. The simple and robust structure with the best parameters can offer a practical and effective solution to the current challenges in shell–seed separation. The findings can contribute to the camellia oleifera fruit processing. A valuable reference can also offer to optimize similar cleaning equipment for other agricultural products. Long-term performance evaluations can be conducted to explore control systems for real-time parameter adjustment under varying material conditions. Sensors and feedback mechanisms can be integrated to enhance separation consistency with less operator dependency, thus scaling up fully intelligent cleaning in the Camellia oleifera fruit industry.