The invention discloses a method for measuring the contents of alkaloids, lignans and nucleosides in the isatis root or preparation thereof by using a quantitative analysis single-maker method. With low-cost stable-structure avaible alkaloids compound (R,S)-epigoitrin as a reference, relative correction factors with lignans compound clemastanin B and nucleoside compounds cytidine, uridine, vernine, and adenosine are established. Therefore, the contents of another five kinds of lignan and nucleoside contents with high content rates are calculated by using the correction factors only by measuring the content of the(R,S)-epigoitrin of the isatis root or preparation, thereby carrying out multi-indicator quality evaluation on the isatis root or preparation simply, conveniently, comprehensivelyand accurately. The quality controllability and curative effect stability of the product can be guaranteed; and the detection cost and time can be saved.