An improved method was developed for enriching arachidonic acid (AA) methyl ester from microbial oil by two-step low-temperature wet fractionation. The effects of solvent, operating temperature, and solvent-to-fatty acid methyl esters (FAMEs) ratio on the enrichment of AA were investigated. The best results were achieved when n-hexane was used as solvent. With operating temperatures in the range −30°C to −80°C and a FAMEs-to-solvent ratio of 1:5 (v/v), the proportion of AA methyl ester isolated could be increased to 83.76±2.78% with a yield of 52.89%. The total recovery of AA methyl ester would be further increased to 90.84% by recrystallization of the solid phases. The 20C, 22C saturated fatty acids were enriched by n-hexane or petroleum ether at −30°C, with concentrations increased 7.5-fold or 7.2-fold compared with their original levels, respectively. In addition, a method that combined alkali and acid catalysis of the transmethylation was the most conducive to the preparation of polyunsaturated fatty acid methyl esters.