‘Akizuki’ (Pyrus pyrifolia Nakai) is a dominant Asian pear cultivar with gradually increasing cultivation area in Shandong province. However, this cultivar is found susceptible to cork spot disorder in recent years. In this study, we explored the physiological-biochemical mechanism of cork spot disorder in pear fruit, and investigated the effectiveness of spraying calcium (Ca), boron (B) solution or prohexadione calcium (P-Ca) on cork spot incidence. Cork spotted fruit had the characteristics of significantly larger fruit size with shorter fruit pedicels. Compared with normal fruit, cork spotted fruit had lower content of total soluble solids, soluble and reducing sugar, and vitamin C. In addition, cork spotted fruit accumulated much higher levels of N and Mg, and lower levels of K and P. However, Ca deficiency was not observed in cork spotted fruit, on the contrary, we determined high concentrations of Ca and free Ca2+ in disordered fruit. At the same time, the ratios of K/Ca, Mg/Ca, and (K+Mg)/Ca were significantly lower in cork spotted fruit as compared with normal fruit. Among all treatments, spraying with 3500 times dilution of P-Ca at 15-day intervals from 30 to 90 days after full bloom showed promise for reducing cork spot incidence in ‘Akizuki’ pear without affecting fruit quality attributes. This research herein reveals the physiological-biochemical characteristic of cork spot disorder, and implicates P-Ca as a potential tool to reduce cork spot incidence in Asian pear cultivar Akizuki.