Pakchoi (Brassica rapa L. Chinensis) is an important cruciferous vegetable crop in East and Southeast Asia. This research aimed to investigate the change of microbial community and antibacterial effect of 405 nm light‐emitting diode (LED405 nm) illumination (15 μ mol/(m2 · s)) against spoilage bacteria on the surface of agar media and fresh‐cut pakchoi. High‐throughput community sequencing was used to quantify bacterial abundance and 16S rRNA was used to analyze the bacterial community composition on fresh‐cut pakchoi treated with or without LED405 nm storage at 4°C. And alkaline phosphatase (AKP) activity and metabolic inhibition assays were selected to measure the mechanism of bacterial inhibition. The results showed that Pseudomonas spp. were able to multiply and cause spoilage of fresh‐cut pakchoi at 4°C. Nevertheless, the majority of Pseudomonas spp. isolated from spoilage pakchoi were Pseudomonas reinekei and Pseudomonas palleroniana which were considered as representative specific spoilage microorganisms in pakchoi. Furthermore, 405 nm light treatment retarded sensory deterioration, inhibited microbial growth. AKP activity and metabolic inhibition assays confirmed the inhibitory effect of light treatment. In brief, 405 nm LED illumination has potential as a preservative to maintain quality, extend the shelf life for 6 days of fresh‐cut pakchoi and abled to control P. reinekei and P. palleroniana growth on fresh‐cut pakchoi at 4°C.