The process of mammalian fertilization involves a series of sperm functional activities, including the sperm transportation, hyperactivation and capacitation, acrosome reaction and sperm-egg fusion, etc. The semen proteins play indispensable roles in these processes, and they are closely associated with the fecundity of males. So these proteins can be biomarkers to evaluate the fertilization capacity of mammalian semen. In this review, we mainly introduce some semen proteins relevant to spermatozoa functions and illustrate their important regulatory roles on the fertilization processes, involving spermatozoa motility, capacitation, acrosome reaction, penetrating the zona pellucida and sperm-egg fusion, etc. Moreover, their potential applications in the evaluation of heredity in livestock are also summarized.