End-to-end speech recognition technology has a simpler and more intuitive framework with better adapta-bility than traditional speech recognition framework.Based on RNN and CTC,this paper implements an end-to-end speech recognition system of Uyghur language via different acoustic unit.We compare this method with the tradi-tional HMM speech recognition framework in a small corpora(THUYG).The experimental results show that the end-to-end speech recognition system based on mono-phone outperforms the HMM-GMM based on mono-phone and triphone by 10.6%and 2.23%lower CER,respectively.