A series of ester‐containing cationic silicone softeners with different alkyl chain lengths were successfully synthesized to manufacture antibacterial cotton fabrics. The relationship between the molecular structure and the softener's mechanical and physical properties was investigated. This study demonstrated that the fabrics treated with SiQCnCl softeners bearing short alkyl chains (n = 9, 11, and 13) showed better instantaneous hydrophilicity, close to that of a pristine cotton fabric. However, the SiQC17Cl‐treated fabrics with long alkyl chains showed the best softness, exceeding that achieved with the conventional finishing agent D1821. And the whiteness index of the fabrics decreased with the use of longer fabric finishing times, with the SiQC15Cl‐treated fabrics exhibiting the highest whiteness index. Moreover, it was also found that SiQCnCl‐treated fabrics showed higher antibacterial activity against Staphylococcus aureus than Escherichia coli, with the SiQC13Cl‐treated fabrics exhibiting the best antibacterial activity. In addition, a model depicting the antibacterial action of the prepared fabrics was illustrated. Finally, it was discovered that the synthesized ester‐containing cationic silicone softener showed better primary biodegradability than D1821 and DC‐5700, exceeding 80% after a 120‐h degradation.