The invention relates to a gene chip for detecting various prawn pathogenes and a detection method thereof. The gene chip is prepared by arranging the probes of a quality control system and the probe points of 18 types of prawn pathogenes on the same solid-phase carrier nylon membrane. The probes of 18 types of the prawn pathogenes comprise probes for detecting 15 types of viruses, probes for detecting fusarium, fish-killing aphanomyces and deformation algal filament cristatum, and probes for detecting Paranophrys and prawn rickettsia. When the gene chip is used for detection, a signal is judged according to the condition whether blue or royal purple appears at a hybridization point by using a digoxin hybridization chromogenic method. The construction of the quality control system on the gene chip ensures the detection specificity and sensitivity, thus, the gene chip can be used for simultaneously detecting various prawn pathogenic microorganisms on the same nylon membrane, has the characteristic of high flux, can replace the prior related detection method for the prawn pathogenic microorganisms, and is a breakthrough of the prior prawn pathogenic microorganism judging technique.