Three kinds of Salen-Mn(Ⅲ) complexes ［Mn(Ⅲ)Lx］CH3COO and three kinds of Salen-Co(Ⅲ) complexes ［Co(Ⅲ)Lx］CH3COO (L1=N,N'-bis (2-Hydroxy-1-naphthaldehyde) o-phenylenediamine, L2=N,N'-bis (2-Hydroxy-1-naphthaldehyde) ethylenediamine, L3=N,N'-bis (2-Hydroxy-1-naphthaldehyde) 1,3-diaminopropane) were synthesized. The results of their fluorescence quenching effect with DNA base show that Mn(Ⅲ) complexes is easier make fluorescence quenching than Co(Ⅲ) complexes with the same base. Quenching intensity is Cytosine>Adenine>Guanine while with the same complexes. The fluorescence quenching selectivity of complexes to bases was presented in the experiment, and the fluorescence quenching could be influenced by the structure of complexes as well.