The invention provides a preparation method of a flexible substrate-GO-metal nanowire composite transparent conductive thin film. The preparation method comprises the steps of quartz glass substrate surface processing, metal nanowire solution preparation, vacuum filtering metal nanowire film, lamination, filtering film removal, GO processing, flexible substrate material solution preparation, flexible substrate film formation and quartz glass substrate stripping. The invention also provides the flexible substrate-GO-metal nanowire composite transparent conductive thin film prepared by the method. The composite transparent conductive thin film prepared by the method has the advantages of low surface peak valley roughness and surface average roughness, good conductivity, high optical transmittance, good mechanical flexibility and good thermal stability, the metal nanowire is firmly attached onto the flexible substrate, the application demand of a device can be achieved, particularly, therequirement of a flexible thin film electronic device on electrode surface roughness can be met, and the reliability and the stability of the metal nanowire electrode in application of the thin film electronic device are improved.