The invention discloses a detection method of multi-drug-resistant microorganisms, the detection method comprises the following steps: capturing the multi-drug-resistant microorganisms by using nucleic acid aptamer magnetic beads, releasing a blocking sequence complementary with an aptamer, converting a protein signal into a nucleic acid signal, amplifying the blocking sequence through an index amplification reaction, and measuring the amplified blocking sequence. According to the invention, a molecular enhancer is added into an index amplification reaction system to inhibit non-specific amplification reaction, and a nanoscale transition metal dihalogen compound is added as a result reading carrier in the determination process, so that the intensity of a background signal is further reduced. The method is simple, convenient and efficient to operate, can achieve the purpose of background-free, rapid and hypersensitive detection, and can solve the key technical problems that a traditional detection technology is long in detection period and low in sensitivity, a background signal exists in a detection result, result interpretation is inaccurate due to the influence of human subjective factors, and severe non-specific amplification exists in isothermal amplification reaction. The method is suitable for detecting the drug resistance of the microorganisms.