Towards the goal of improving the tribological properties of epoxy-based composites, epoxy resin was firstly modified with carboxyl terminated butadiene acrylonitrile (CTBN), and then further modified by core-shell structured of SiO2@MoS2 fillers. The friction and wear properties of studied composites were tested on a Plate-on-Ring configuration under different loads and speeds. To reveal the tribological contribution of MoS2 and SiO2 in the hybrid fillers, tribo-tests were also done on composites filled with single CTBN, MoS2 and SiO2. It is revealed that the transfer of both the EP/CTBN matrix and SiO2@MoS2 CSs fillers play an important role in governing the tribo-properties of rubber toughened EP composites. Depending on contacting conditions, the SiO2@MoS2 CSs fillers might be released into the sliding interface and tribo-chemical reactions might take place, both of which helped improve the tribo-properties of studied composites.