Aggregation of amyloid-beta (A beta) peptides into prefibrillar toxic oligomers is responsible for Alzheimer's disease, which is one of the most commonly known forms of neurodegenerative diseases. It has been reported that the low-molecular weight A beta(1-42) trimer and its higher order oligomers are responsible for the cytotoxicity in the neuronal cells, leading to their death. Various experimental studies have shown that boron nitride nanotube (BNNTs) are noncytotoxic for health and environment and biocompatible in living cells and can be used as delivery vehicles for brain anticancer drugs. Here, we investigate the effects of BNNT on the secondary structure of A beta(1-42) in the amyloid oligomerization process. We have performed long atomistic molecular dynamics simulations of 4.0 mu s in total to study the structural stability of A beta(1-42) trimer both in presence and absence of BNNT in explicit solvent. It is found that in the absence of BNNT, A beta(1-42) trimer aggregates, leading to alpha-helix to beta-sheet transition, whereas BNNT provides structural stability to the peptides by keeping them separated and preserving the initial monomeric helical conformation of the A beta(1-42) trimer. It is found through a free-energy decomposition analysis that the key residues (Lys28, Ile31, Ile32, Leu34, Val40, and Ile41) from the C-terminal that are more responsible for beta-sheet fibril formation bind with the BNNT surface and block their structural conversion. Due to the presence of polar B-N bonds, BNNT is less hydrophobic as compared with the carbonaceous nanomaterials where large hydrophobicity of these carbonaceous nanomaterials mostly destabilizes the secondary structure of peptides. The current study reveals that the less hydrophobicity of BNNT provides stability of the initial secondary structure of the A beta(1-42) trimer and hinders their aggregation. Hence, the secondary structure stabilization in presence of BNNT provides new possibilities for the design of different nanoparticles as therapeutic agents for different types of amyloidogenesis by tuning their hydrophobicity.