Abstract The poor compatibility between crumb rubber (CR) and asphalt matrix always brought difficulties to the engineering application of CR modified (CRM) asphalt. The compatibility in CRM asphalt was universally characterized by storage stability test at a macroscale. Actually, the term “compatibility” was introduced to describe the “level of interaction” between the asphalt and polymers in polymer modified asphalt. Therefore, in this study, the compatibility in CRM asphalt (i.e., the level of asphalt-rubber interaction) was newly characterized by removing the CR particles in the CRM binder through a customized drainage process and quantifying the difference between drained asphalt and base asphalt. In practical terms, the changes in the rheological properties and chemical composition of binder relative to base asphalt were measured by dynamic shear rheometer and gel permeation chromatography, respectively. Based on this novel characterization, it was found that smaller CR particles tended to possess greater compatibility with asphalt, and the asphalt with a higher percentage of light fractions was expected to be more compatible with CR particles. On the other hand, the result of the conventional hot tube test found the storage stability mainly depended on the size and content of CR particles. Furthermore, a strong statistical correlation between the novel characterizations (i.e., changes in rheology and chemistry of binder) and the common characterization (i.e., storage stability) was found, and its essential cause was discussed. Therefore, this novel characterization could provide another reliable and simple way to evaluate the compatibility in CRM asphalt.