Time-resolved spectra of six kinds of ruthenium polypyridyl complexes ［Ru(L)2(R)］2+（L=bpy， phen， bpy=2,2’-bipyridine, phen=1,10-phenanthroline， R=7-CH3-dppz， 7-F-dppz， dpbpd(NH2)2） bonding to calf thymus DNA in aqueous solution were compared and analyzed by using the three energy level kinetic model. And the effects of the substituent groups on the interaction ways for the ruthenium complexes bonding to DNA were discussed. The result shows that first, the six complexes all show two binding modes on bonding to DNA, i.e. the side-on binding mode and the perpendicular binding mode, and the later one is considered as a main binding way. Second, the properties of substituent groups have an important impact on the relative weight of the two binding modes. The conclusion offers a dynamics argument to study the interaction mechanism for the complex bonding to DNA further.