Self-assembling amphipathic peptides (SAPs) are a kind of functional peptides, which have alternating hydrophilic and hydrophobic residues and can affect the thermal stability and catalytic properties on the fused enzymes. In this study, several SAPs fusion protein which comprised S1 peptide (AEAEAKAKAEAEAKAK) derivatives and Bacillus sp.WSHB04-02 alkaline polygalacturonatelyase (PGL) or PGL-S1 with different linker peptides were constructed, and the effect of the linker peptides and the amino acids composition of SAPs on expression quantity the fusion enzymes were examined. The results showed that the hydrophobicity of hydrophobic amino acids make a critical difference on the expression quantity of PGL. The SAPs which contained the weaker hydrophobic alanine and glycine residues could make the fused protein expressed normally. The PGL-S1v1 possessed the relative high crude enzyme activity. Compared with the PGL and PGL-S1, the extracellular enzyme activity was increased by9-fold and 1.5-fold, respectively. As for the linker peptides, the flexible linkers enhanced the extracellular expression of the fusion protein more efficiently compared with the rigid counterparts. Of which the crude enzyme activity of PGL-F-S1 with flexible linker peptide were increased 14-fold than that of PGL. These results suggested that the amino acids composition of SAPs and the flexibility of the linker peptides could effectively affect the expression quantity the fusion protein.