Schottky junctions based on one-dimensional semiconductor nanomaterials, such as nanowires (NWs) and nanobelts (NBs), have been widely used in building high-performance nano-electric and nano-optoelectric devices during the past 15 years. Meanwhile, with considerable development in diverse application fields, more and more interests are turning to the investigation of the fundamental physics inside the junctions. The inhomogeneity of the interface between semiconductor NWs/NBs and metal electrodes has significant influence on the electrical transport mechanism of Schottky junctions. However, few researchers are involved in such studies and the physical mechanism here is far from fully understood. In this work, we fabricated Schottky junctions based on single CdSe NWs, in which Au was used as a Schottky contact with CdSe NW. The temperature dependence of the electrical transport characteristics of typical CdSe NW/Au Schottky junctions were characterized. The ideality factor was found to decrease and the zero-bias Schottky barrier height (SBH) increased monotonously as the temperature was increased from 140 to 320 K, and this relationship was ascribed to SBH inhomogeneity. The electrical transport mechanism was analyzed quantitatively with a spatial potential fluctuation model, in which SBHs obey the Gaussian distribution. The standard deviation of the SBH distribution was determined to be as high as 13.54% and 13.94% of the zero-bias mean SBH in the temperature ranges 140-200 K and 200-320 K, respectively. Our work revealed the barrier inhomogeneity at CdSe NW/Au interfaces and its influence on the electrical transport mechanism of NW-based Schottky junctions.