To overcome the outer membrane barrier that restricts endolysin efficacy against Gram-negative bacteria such as Pseudomonas fluorescens, the natural compound cinnamaldehyde could be employed as a membrane-permeabilizing agent to destabilize this protective layer. This study quantified the synergistic interaction between the novel endolysin LysPFX32 and cinnamaldehyde using the fractional inhibitory concentration index (FICI). The antibacterial mechanisms of endolysin and cinnamaldehyde were investigated by assessing outer and inner membrane integrity, observing morphological changes via scanning electron microscopy (SEM), monitoring membrane permeability using confocal laser scanning microscopy (CLSM), analyzing DNA-binding capacity, and profiling transcriptional responses through qPCR. The results demonstrated significant synergy, with a FICI of 0.425, which reduced the required concentration of LysPFX32 by 16-fold. The combined treatment compromised both the outer and inner membrane integrity, resulting in the leakage of intracellular nucleic acids (127.73 ng/μL) and proteins (87.45 mg/mL). Furthermore, the combined treatment demonstrated potent anti-biofilm activity, with a 56.07% inhibition rate against biofilm formation and a 66.7% removal rate for mature biofilms, while also downregulating key genes associated with quorum sensing, biofilm development, and motility (specifically pcoI, pcoR, and fliI). In food models, the synergistic treatment effectively suppressed the growth of P. fluorescens, which reduced total volatile basic nitrogen (TVB-N) production and extended the product shelf life by 4 days. This study proposes a novel and natural biological strategy, which is mechanistically complementary, for controlling spoilage bacteria. It offers a promising natural preservative solution for the food industry.