The storage stability concern, caused by phase separation for the density difference between polymers and asphalt fractions, has limited the widespread application of polymer modified asphalt (PMA). Therefore, this study aims to improve the storage concern of PMA by incorporating nano-montmorillonite. To this end, different nano-montmorillonites were incorporated to three PMAs modified with three typical asphalt modifiers, i.e., crumb rubber (CRM), styrene–butadiene-rubber (SBR) and styrene–butadiene-styrene (SBS). A series of laboratory tests were performed to evaluate the storage stability and rheological properties of PMA binders with nano-montmorillonite. As a consequence, the incorporation of nano-montmorillonite exhibited a remarkable effect on enhancing the storage stability of the CRM modified binder, but limited positive effects for the SBR and SBS modified binders. The layered nano-montmorillonite transformed to intercalated or exfoliated structures after interaction with asphalt fractions, providing superior storage stability. Among selected nano-montmorillonites, the pure montmorillonite with Hydroxyl organic ammonium performed the best on enhancing storage stability of PMA. This paper suggests that nano-montmorillonite is a promising modifier to alleviate the storage stability concern for asphalt with polymer modifiers.