The invention discloses a brand-new fermentation method of FR901379. According to the method, methyl palmitate is added as a side chain precursor of FR901379 fatty acid in the fermentation process ofFR901379 to promote biosynthesis of FR901379. At the same time, soybean lecithin insoluble in a reaction solution is introduced into a fermentation broth. Besides serving as a fermentation precursor,methyl palmitate also serves as an oxygen carrier in the fermentation system together with soybean lecithin, so that resistance of gas-liquid oxygen transfer is reduced, the problem of insufficient dissolved oxygen in the fermentation process in the prior art is solved, the fermentation yield of FR901379 is increased, and the production cost is reduced.