The invention provides a method for identifying a fertilization mode of an ictalurus punctatus culture pond, which comprises the following steps of: extracting total DNA (deoxyribonucleic acid) of intestinal microorganisms of the ictalurus punctatus in the culture pond, designing a primer aiming at a DNA sequence of 16S rDNA (ribosomal deoxyribonucleic acid) gene of a Lactobacillus population by taking the total DNA as a template, performing PCR (polymerase chain reaction) amplification, and judging that inorganic fertilizer is used in the culture pond if an amplification product does not have a 1054bp band. According to the method for identifying the fertilization mode of the ictalurus punctatus culture pond, the channel catfish pond fertilization mode can be rapidly, simply, accurately and effectively identified, the operation is simple, the cost is low, the accuracy is high, the identification result is stable and reliable, and the problem that the channel catfish fertilization mode is difficult to identify can be solved.