Many special honeys are produced in Yunnan province due to abundant nectar plants and minerals resources provided by the unique natural environment in this area. In this work, the physicochemical property of three honeys (Viciacracca honey, Hevea brasiliensis honey and Punica granatum honey) from Yunnan was studied. The results showed that in different honeys the moisture content, electrical conductivity and dynamic viscosity were different. The sugar contents of each honey were determined with HPLC-RI. The results showed that P. granatum honey had the most abundant glucose ［35.62 g·(100 g)-1］, and H. brasiliensis honey had the most abundant fructose ［41.03 g·(100 g)-1］. Thirteen different mineral elements in three honey species were determined with FAAS. It was found that the mineral level was from 167.24 mg·kg-1 in P. granatum honey to 437.34 mg·kg-1 in H. brasiliensis. Based on the mineral content the three honey species were classified following the principal component analysis (PCA) method. The result showed that Cu, Zn and Na could act as the elemental markers for V. cracca honey, while Mg, K, Ca, As and Cd act as the elemental markers for H. brasiliensis honey, and Fe, Mn, Ni, and Cr act as the elemental markers for P. granatum honey. This study reported the physicochemical property of three special Yunnan honeys, which could help the further study and utilization of these honeys.