Fixed and mobile global navigation satellite system (GNSS) reference stations are the main differential positioning resources for automated steering system in China at current stage. However, with the rapid increase in GNSS reference stations usage, there is an increasing trend of serious radio frequency interference, which mainly due to deficiency of technical and management coordination. To solve this problem, a cloud based architecture that achieved regional GNSS reference stations management and information sharing for agricultural applications was proposed. Shihezi, a district of Xinjiang, was selected as the study area. The accurate information (i.e., name, position, and frequency) of 84 fixed reference stations from three enterprises was collected, based on which the difference of distance (ΔD) and the difference of frequency (ΔF) between each two reference stations were calculated. By using ΔD and ΔF, redundancy and frequency interference were analyzed, coordinate adjustment of two stations were conducted, and the prototype system and an APP were developed for reference station management and agricultural applications. The results showed that the 84 reference stations occupied 26.7MHz frequency band with 47 frequencies, and 30 of which were independent frequency. In addition, there were 18 couples of stations using the same frequencies and 29 pairs of stations using near frequencies（ΔF≤25kHz） within 40km in northeast of Shihezi. The average redundancy was 263.2%, and the redundancy of central area was even worse. To benefit from the redundancy information, it was utilized to adjust the coordinate of the GNSS reference station in order to improve the reliability of differential signal access. Three stations were tested and the precision to millimeter level and centimeter level for longitude and latitude respectively, which meant the coordinate adjustment can improve the accuracy of GNSS reference stations. The prototype system and APP achieved the functions such as stations recording, interference detection, station construction assistance, and frequency recommendation, and it can improve the management efficiency of GNSS reference stations and reduce radio frequency interference.