Modification of saponite (Sap) by surface engineering and intercalation chemistry introduces guest species into the structure of Sap and enhances the functionalities of the resultant Sap-based hybrids or composites. This review summarizes and evaluates latest scientific advances in the strategies for surface engineering, intercalation and hybridization of Sap, the insights into the relevant mechanisms, and the properties and applications of the resultant Sap-based materials. Studies have indicated that Sap can be inorganically modified by acid activation, inorganic cation exchange, pillaring, and adsorption. The methods of preparing organo-saponite (OSap) hybrids can be categorized as follows: 1) exchanging the inorganic cations in the interlayer space of Sap with organic cations; 2) covalent grafting of organic moieties or groups onto the surface of Sap; 3) intercalating polymer into the interlayer space of Sap by solution intercalation, and melt mixing or in situ polymerization. Organic-inorganic modified Sap can be made through the reactions between organic species and inorganic-modified Sap, or by the combination of inorganic species with organic-modified Sap. Modified Sap exhibits exceptional thermal stability, surface acidity, optical effects and adsorption. As such, the modified Sap can be used for optical materials, adsorbents, catalysts and clay/polymer nanocomposites (CPN). Literature survey suggests that future studies should place emphasis on optimizing and scaling up the modification of Sap, probing the thermodynamics, kinetics and mechanisms of the modification of Sap, endowing Sap with novel functionalities, and accordingly advancing the practical applications of the resultant Sap-based materials.