The aim of this study was to investigate the effect of partial solar eclipse on the carbon metabolic diversity of airborne microorganisms. We used Biolog metabolic fingerprinting method to analyze the variation of the carbon metabolic diversity of airborne microbial community in Urumqi before and after partial solar eclipse. The results suggested that the ability of carbon sources utilization for microbes on the day was higher than other days. The analysis of variance of the microbial community diversity indices showed that Shannon-Wiener diversity was the highest on the day; and principal component analysis demonstrated that carboxylic acids was the mainly carbon sources to the differentiation of the airborne microorganisms. Hence partial solar eclipse may affect the functional diversity of air microbial community in Urumqi.