Source dependency information has been successfully introduced into statistical machine translation. However, there are only a few preliminary attempts for Neural Machine Translation (NMT), such as concatenating representations of source word and its dependency label together. In this paper, we propose a novel NMT with source dependency representation to improve translation performance of NMT, especially long sentences. Empirical results on NIST Chinese-to-English translation task show that our method achieves 1.6 BLEU improvements on average over a strong NMT system.