•VOCs from strain ZL3 exhibited excellent antifungal activities.•The VOCs had potential against postharvest gray mold.•Twenty-three VOCs were detected by using SPME coupled with GC–MS. Postharvest gray mold is the most devastating fungal disease, and could lead to enormous losses on Chinese cherry. To formulate an effective and environment friendly management strategy for postharvest gray mold, an endophytic bacterial strain ZL3 with excellent antifungal activity was screened by using dual culture method. Strain ZL3 was identified as Pseudomonas chlororaphis based on 16S rRNA and gyrB gene sequence analysis. The maximum percent of mycelial growth inhibition (PGI) of VOCs to B. cinerea was up to 97.23% under the antifungal conditions (temperature of 31.96 °C, pH of 6.74 and glucose of 25.96 g/L) optimized by using Box-Behnken Design (BBD) of response surface method (RSM). The biological efficiency of VOCs was performed on cherry fruit at 0 °C for 21 d and 25 °C for 7 d. At 25 °C and 0 °C, the disease incidence reduced to 31.67% and 21.67%, whereas the lesion diameter decreased to 0.60 cm and 0.32 cm, respectively. Additionally, twenty-three VOCs, including 6 alkanes, 4 aldehydes and ketones, 4 alcohols, 4 alkenes, 3 acids & esters, 1 aromatic compound, and 1 sulfur compound, were detected by gas chromatograph-mass spectrometry (GC–MS). It is noticed that most VOCs, except for 1, 10-undecadiene and 1-dodecene, demonstrated significant differences among different collection time. The results of this work suggested that strain ZL3 could be used as a promising biocontrol agent to control postharvest gray mold on Chinese cherry.