Taking the advantage of well dispersing ability and unique pore plugging capacity, nanomaterials have been extensively used as filtration control additives in water-based drilling fluids (WBDFs). However, nanomaterials are seldom robust when exposed to high temperature and salinity which restricts their applications. Herein, we synthesize two inorganic/organic hybrid nanomaterials using silica as the core and grafted with zwitterionic polymer on the surface (ZSHNM-1 and ZSHNM-2), and conduct in-depth research on their filtration performance. ZSHNM exhibits bead- and necklace-like structures, adsorbs onto and promotes the homogenous dispersion of montmorillonite irrespective of the presence of salt, and facilitates the formation of filter cake with remarkably low permeability, according to experimental results and DFT simulation results. Notably, ZSHNM-2 has significantly stronger thermal resistance up to 250 °C, salt tolerance as high as 11 wt%, which is expected to use in filed applications of ultra-deep wells. It is attributed to the more appropriate particles size distribution and longer polymer tails, efficiently plugging the pores. In addition, these nanomaterials had high polyamine rejection, whereas had little influence on KCl, which should be paid attention to selecting shale inhibitors. This study can be a guide to technically related areas where nanomaterials are used extensively.