A new statistical method called "bilingual chunking" for structure alignment is proposed. Different with the existing approaches which align hierarchical structures like sub-trees, our method conducts alignment on chunks. The alignment is finished through a simultaneous bilingual chunking algorithm. Using the constrains of chunk correspondence between source language (SL)1 and target language (TL), our algorithm can dramatically reduce search space, support time synchronous DP algorithm, and lead to highly consistent chunking. Furthermore, by unifying the POS tagging and chunking in the search process, our algorithm alleviates effectively the influence of POS tagging deficiency to the chunking result. The experimental results with EnglishChinese structure alignment show that our model can produce 90% in precision for chunking, and 87% in precision for chunk alignment.