Boron in the form of potassium tetraborate was effective for control of blue mold rot caused by Penicillium expansum in jujube fruit. The control activity was positively correlated with the concentration of boron solution. Boron at 0.5% enhanced the biocontrol efficacy of the antagonistic yeast Cryptococcus laurentii against P. expansum. Analysis of population dynamics demonstrated that growth of C. laurentii was not significantly influenced by boron in the fruit wounds. C. laurentii multiplied quickly, regardless of whether the yeast was used alone or combined with boron. An in vitro study showed that boron at 0.25% even stimulated the growth of C. laurentii at the end of incubation period. By comparison, mycelial spread of P. expansum in the culture medium was completely inhibited by boron at 0.25%. Using the fluorescent probe rhodamine 123, we found that the mitochondrial membrane potential collapsed significantly after boron treatment. This indicated that boron inhibited the growth of P. expansum by targeting the mitochondria of the fungal pathogen. Taken together, our data suggest that the enhancement in biocontrol efficacy of C. laurentii may be related to the differential influence of boron on the antagonistic yeast and the fungal pathogen.