We propose a novel technique of learning how to transform the source parse trees to improve the translation qualities of syntax-based translation models using synchronous context-free grammars. We transform the source tree phrasal structure into a set of simpler structures, expose such decisions to the decoding process, and find the least expensive transformation operation to better model word reordering. In particular, we integrate synchronous binarizations, verb regrouping, removal of redundant parse nodes, and incorporate a few important features such as translation boundaries. We learn the structural preferences from the data in a generative framework. The syntax-based translation system integrating the proposed techniques outperforms the best unconstrained system in NIST-08 evaluations by $1.3$ absolute BLEU, which is statistically significant.