With the completion of the model plant genome sequencing projects such as Arabidopsis and rice (Oryza sativa L.), comparative genomics has been developed rapidly in recent years. As a new branch of science, this technique has offered a new approach for studying plant genome evolution, structure and function. In this paper, the research strategies, such as comparative genetic mapping, microcollinearity study in gene structure, comparative research on the ESTs and proteins, comparative QTL mapping among crops, and comparative map-based cloning of genes, were summarized. We reviewed the principles, characteristics, feasibilities and progresses of various strategies that were used in plant comparative genomics. It would be helpful to use the sequence data from model plants to elucidate the structure and function of other crop genomes.