The Chinese mitten crab (Eriocheir sinensis), recognized as a high-value aquatic product, necessitates effective cleaning to ensure both safety and quality. Conventional cleaning methods frequently fail to eliminate biofilms and pathogenic bacteria, such as Aeromonas hydrophila, which pose significant health risks and contribute to spoilage. This study explores the bactericidal efficacy and underlying mechanisms of ultrasound treatment combined with a lactic acid and malic acid complex solution for decontaminating crabs and enhancing food safety. Employing a range of methodologies, including microscopic imaging, live/dead staining, RT-qPCR, and texture and microstructure analysis, the results indicate that the combined treatment significantly reduced A. hydrophila counts by 4.16 lg CFU/mL and induced substantial bacterial membrane damage, as evidenced by scanning electron microscopy (SEM). Gene expression analysis revealed a pronounced downregulation of biofilm-related genes. Notably, the treatment also preserved the texture and sensory properties of crab meat, thereby ensuring high product quality. These findings suggest that the application of ultrasound in conjunction with a lactic acid-malic acid solution represents a green and effective strategy for improving food safety and quality in the processing of aquatic products, offering a sustainable and eco-friendly alternative to traditional cleaning methods.