In phrase-based machine translation (PBMT) systems, the reordering table and phrase table are very large and redundant. Unlike most previous works which aim to filter phrase table, this paper proposes a novel deep neural network model to prune reordering table. We cast the task as a deep learning problem where we jointly train two models: a generative model to implement rule embedding and a discriminative model to classify rules. The main contribution of this paper is that we optimize the reordering model in PBMT by filtering reordering table using a recursive autoencoder model. To evaluate the performance of the proposed model, we performed it on public corpus tomeasure its reordering ability. The experimental results show that our approach obtains high improvement in BLEU score with less scale of reordering table on two language pairs: English-Chinese (+0.28) and Uyghur-Chinese (+ 0.33) MT.