Molecular dynamics simulation is among the most significant methods in nanoscale studies. This paper studied the effect of strain rate, temperature, and nanotube chirality on the stress-strain behavior of aluminum/silicon nanotubes (SiNTs) using molecular dynamics simulation. Ultimate tensile stress and Young’s modulus of the nanocomposite were evaluated using molecular dynamics simulation. According to the results, Young’s modulus of the nanocomposite decreased with increasing temperature. Also, Young’s modulus decreased by increasing the strain rate. Next, an experimental approach was used based on the Box–Behnken design. According to the input parameters and the experimental approach, the number of simulations in the software was 39 runs. Overall, it is concluded that the optimal conditions were created at a temperature of 50 K, a strain rate of 0.01/ps, and chirality of (5,5), leading to the elasticity modulus of 137 GPa and the ultimate tensile stress of 11.8 GPa.