The invention discloses a method for fermenting and deodorizing anchovy fish oil microorganisms. The method comprises the following steps: firstly suspending a strain SJA in pure water, and then transferring the pure water with the strain SJA into an anaerobic jar; controlling the pH value at 6.5 to 7.2, controlling the temperature at 30 to 37 DEG C, adding anchovy oil, and adequately stirring and mixing; finally standing and layering the anchovy oil under the protection of the high-purity nitrogen of 99.99 percent, and split charging the oil layer into a sample barrel to obtain the deodorized anchovy fish oil. By adopting the deodorization method, small-molecular odor substances take part in bacterial anabolism to be converted into odorless substance by virtue of the metabolism of the microorganism strain SJA, or the small-molecular odor substance is subjected to molecular structure modification under the effect of the microorganism enzyme, so that the odor substance is converted to the odorless substance, and the permanent deodorization can be achieved.