Boron nitride nanotubes (BNNTs) are promising reinforcing fillers for ceramics because of their extraordinary structural and mechanical properties and thermal stability, but their reinforcing mechanisms remain elusive. Here, we investigate how BNNTs reinforce silica nanocomposites by quantifying their bulk and interfacial mechanical properties using in situ Raman micromechanical characterization techniques and microstructural analysis. Our studies reveal that the incorporation of small amounts of BNNTs (0.1 to 0.5 wt %) substantially increases the flexural strength (∼51 to ∼153%) and fracture toughness (∼54 to ∼167%) of silica. The effective interfacial shear stress in the bulk BNNTsilica nanocomposite follows a shear-lag model, with a maximum value of ∼92 MPa. The microstructural analysis reveals that incorporating BNNTs in silica has a prominent influence on its crystallization, with a noticeable increase in porosity and a decrease in crystal size and lattice strain. The collective microstructural changes substantially contribute to the bulk mechanical properties of the BNNT-silica nanocomposite. These findings provide insights into the reinforcement mechanism of BNNTs in ceramics and contribute to the optimal design of light, strong, tough, and durable ceramic materials.