In order to study the affinity differences of hybrid cassava between different parents, respectively, South China 5, South China 6 and South China 7 were as the materials, to conduct reciprocal cross, then fertility rates was calculated between different combinations. The proteins from stigma after fertilization were also analyzed, due to exploring the regulation mechanisms of stigma influence on hybridization affinity. The results showed that: fertility rates in SC5 (♀)× SC7 (♂) was highest, 26.22%, while SC7(♀) × SC5(♂) was lowest, 11.13%. By two-dimensional electrophoresis and mass spectrometry analysis of pollinated stigma protein changes in female parent SC5 and SC7, 27 differential expression proteins were identified in which 19 were up-regulated, these differentially expressed proteins involved in carbon metabolism and energy metabolism, molecular chaperone and amino acid metabolism, while 8 protein spots were down-regulated, its involved in protein synthesis and hydrocyanic acid metabolism. It indicated that these metabolic processes were related with high affinity of cassava.