The invention discloses a method for transforming schizochytrium limacinum by agrobacterium tumefaciens and application, and the transformation method comprises the following steps: introducing an exogenous gene into the agrobacterium tumefaciens, and introducing the exogenous gene into the schizochytrium limacinum by utilizing the agrobacterium tumefaciens, so that the schizochytrium limacinum obtains the function of the related exogenous gene. According to the invention, the agrobacterium AGL-1 transferred into a G418 resistance gene expression cassette and the schizochytrium limacinum HX-308 are co-cultured, so that an exogenous gene is successfully transformed into the schizochytrium limacinum HX-308, and fixed-point knockout of the gene is realized. Experimental operation is very simple, time and cost are effectively saved, Agrobacterium tumefaciens can be converted into schizochytrium limacinum, more importantly, gene knockout can be achieved, and a set of complete genetic operating system can be constructed in the schizochytrium limacinum through gene knockout. According to the invention, site-specific integration can be completed by using a short homologous arm, and a 2-3kb homologous arm is possibly needed in general fungal transformation, so that a foundation is laid for simplifying genetic manipulation of schizochytrium limacinum.