Endowing epoxy coatings with long-term anticorrosion performance is extremely important and urgent for its application in extreme marine environment. We prepared a new composite nanofiller to realize this purpose. Mesoporous silica nanocontainers (MSNs) are prepared by sol-gel method. The corrosion inhibitor (BTA) is loaded in the MSNs to give the self-healing ability of the nanofiller. To realize controllable release of BTA, chitosan (CS) is coated on the surface of the MSNs-CS. To improve the dispersion ability of the MSNs-CS nanofillers in epoxy coatings, the fillers are loaded on the surface of 2D nanoflakes of TpPa. The results show that the coated CS can act as a pH response valve to control the release of the loaded BTA. The TpPa can not only improve the dispersion ability of MSNs in epoxy coatings, but also it can act as physical barrier to prevent the diffusion of corrosive media. The controllable release of BTA gives the coatings self-healing ability. After 90 days of immersion, results show that the low-frequency impedance modulus of MSNs-CS/TpPa-1 wt% reaches 7.68 × 109 Ω cm2, and the low-frequency impedance modulus of MSNs-1 wt% and COF-1 wt% are only 6.74 × 107 Ω cm2 and 1.24× 107 Ω cm2, respectively. In the abrasion resistance test, the averaged friction coefficient of MSNs-CS/TpPa-1 wt% is as low as about 0.35 and has the smallest wear area of 125 μm2. It proves that it has good anti-wear performance. This work provides a new nanofiller to enhance the long-term protection performance of epoxy coatings.