In this work, we report a study on the relationship between flux and intensity for molecular clouds. Our analysis is established on high-quality CO images from the Milky Way Imaging Scroll Painting project. The new flux–intensity relation characterizes the flux variation of molecular clouds above specific intensity levels. We found that the flux–intensity relation exhibits two prominent features. First, the flux–intensity relation generally follows exponential shapes; second, hierarchical structures of molecular clouds are imprinted on flux–intensity relations. Specifically, 12CO flux–intensity relations are composed of one or more exponential segments, and for molecular clouds with segmented flux–intensity relations, the edge and the flux of the high-temperature component are strikingly consistent with 13CO emission. Further analysis shows that a similar relationship also exists between 13CO flux–intensity relations and C18O emission. The mean brightness temperature of molecular clouds is tightly associated with the decay rate of flux, the break temperature of exponential segments, and, to a certain extent, the flux fraction of the high-temperature component. Broadly, the flux–intensity relation of a molecular tracer, either in optically thick or in optically thin cases, has the capability to outline the silhouette of internal structures of molecular clouds, proving to be a potent tool for probing structures of molecular clouds.