With binomial coefficient smoothing and Morlet wavelet analysis, the anomaly time characteristics, inter-annual climate, and the spatio-temporal-varying characteristics of the temperature anomalies were analyzed using air temperature observations from stations in South Xinjiang from 1951 to 2007. The results show a pronounced difference in air temperature between winter and summer, mainly negative anomalies before the 1980s and a change to positive temperature anomalies after the 1980s; after 2000 a cooling trend appeared. The temperature deviation in summer was less than that in winter; this deviation appears in two waves during the 57-year period. Abnormally warm periods occurred in the late 1950s, the late 1970s, and at the beginning of this century, showing a 20-25-year oscillation. The frequency of abnormal temperature was 30% in winter and 26% in summer. There were more cold winters than warm winters, and more hot summers than cooler summers. More cold years appeared in the 57-year period than warmer ones and the extent of lower air temperature was greater than that of higher air temperature. The winter temperature in South Xinjiang showed two significant oscillations: a 6-10-year inter-annual cycle and an 18-20-year inter-decadal cycle. The summer temperature showed one significant oscillation: a 20-year inter-decadal cycle. The distribution of temperature and abnormal temperature varied with different decades and seasons. However, according to the long-term trend of air temperature, the region north of South Xinjiang (southern Tianshan Mountain) became hotter, while the Tarim basin and the region south of South Xinjiang became cooler. The temperature-ascending extent in winter was greater than that in summer in the calefactive area while the temperature-descending extent in summer was greater than that in winter in the descensional area.