More than 240 items of historical records containing climatic information were retrieved from official historical books, local chronicles, annals and regional meteorological disaster yearbooks. By using moisture index and flood/drought (F/D) index obtained from the above information, the historical climate change, namely wet-dry conditions in borderland of Shaanxi Province, Gansu Province and Ningxia Hui Autonomous Region (BSGN, mainly included Ningxialu, Hezhoulu, Gongchanglu, Fengyuanlu and Yan’anlu in the Yuan Dynasty) was studied. The results showed that the climate of the region was generally dry and the ratio between drought and flood disasters was 85/38 during the period of 1208–1369. According to the frequencies of drought-flood disasters, the whole period could be divided into three phases. (1) 1208–1240: drought dominated the phase with occasional flood disasters. (2) 1240–1320: long-time drought disasters and extreme drought events happened frequently. (3) 1320–1369: drought disasters were less severe when flood and drought disasters happened alternately. Besides, the reconstructed wet-dry change curve revealed obvious transition and periodicity in the Mongol–Yuan Period. The transitions occurred in 1230 and 1325. The wet-dry change revealed 10- and 23-year quasi-periods which were consistent with solar cycles, indicating that solar activity had affected the wet-dry conditions of the study region in the Mongol–Yuan Period. The reconstructed results were consistent with two other study results reconstructed from natural evidences, and were similar to another study results from historical documents. All the above results showed that the climate in BSGN was characterized by long-time dry condition with frequent severe drought disasters during 1258 to 1308. Thus, these aspects of climatic changes might have profound impacts on local vegetation and socio-economic system.