Neural Machine translation has shown promising results in recent years. In order to control the computational complexity, NMT has to employ a small vocabulary, and massive rare words outside the vocabulary are all replaced with a single unk symbol. Besides the inability to translate rare words, this kind of simple approach leads to much increased ambiguity of the sentences since meaningless unks break the structure of sentences, and thus hurts the translation and reordering of the in-vocabulary words. To tackle this roblem, we propose a novel substitution-translation-restoration method. In substitution step, the rare words in a testing sentence are replaced with similar in-vocabulary words based on a similarity model learnt from monolingual data. In translation and restoration steps, the sentence will be translated with a model trained on new bilingual data with rare words replaced, and finally the translations of the replaced words will be substituted by that of original ones. Experiments on Chinese-to-English translation demonstrate that our proposed method can achieve more than 4 BLEU points over the attention-based NMT. When compared to the recently proposed method handling rare words in NMT, our method can also obtain an improvement by nearly 3 BLEU points.