Aspergillus niger lipases are important biocatalysts widely used in industries for food processing and pharmaceutical preparation. High-level expression recombinants can lead to cost effective lipase large scale production. Total gene synthesis is an efficient method to enhance the expression level of the gene. According to the mature peptide sequence of A. niger lipase and codons of preference in Pichia pastoris, 26 primers with 20bp overlaps at both 57 and 37 ends between adjacent oligonucleotides were designed and synthesized. Fragments lipA1(300bp), lipA2(237bp), lipA3(234bp) and lipA4(210bp) were separately synthesized by assembly PCR, and then they were used as the template to get the full length gene. The synthetic gene was cloned into pPIC9K secretory expression vector. The expression efficiency was verified with analysis of mRNA secondary structure using RNA Structure 4.5.