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This paper describes the EBMT system of Kyoto University that participated in the OLYMPICS task at IWSLT 2012. When translating very different language pairs such as Chinese-English, it is very important to handle sentences in tree structures to overcome the difference. Many recent studies incorporate tree structures in some parts of translation process, but not all the way from model training (alignment) to decoding. Our system is a fully tree-based translation system where we use the Bayesian phrase alignment model on dependency trees and example-based translation. To improve the translation quality, we conduct some special processing for the IWSLT 2012 OLYMPICS task, including sub-sentence splitting, non-parallel sentence filtering, adoption of an optimized Chinese segmenter and rule-based decoding constraints.