Mesoporous molecular sieve materials have been widely studied in academic and industry due to their remarkable physicochemical properties, including the high specific surface area and pore volume, extensively pore structure, controllable morphology, surface functionalization, good thermal stability, non-toxic and harmless. Ordered mesoporous silica materials, prepared by template method, possess well-ordered periodicity and one dimension to three dimensional interconnected pore structures that are of interest for numerous applications, such as adsorption, separation, catalysis and biomedicine engineering. In order to utilize the geometric and electronic bound properties of ordered-mesochannels as micro reactor, it is necessary to develop host-guest assembly from fundamental and application point of view. In this review, combining with the latest work in our group, ordered mesochannels of mesoporous silica materials are used as a base and starting point. The research progress of host-guest assembly in recent years are introduced systematically. Influence factors, including the choice of templates, organic groups and guest, preparation methods and other necessary modifications, and synthetic mechanism in the process of host-guest assembly are also discussed. Finally, host-guest assembly of ordered mesoporous silica materials in environmental purification and biomedical engineering application are summarized.