The determination of mechanical properties at the nanoscale is of such importance today that researchers pay special attention to it. Discovering the mechanical properties of biological composite structures in the nanoscale is much interesting today. Top neck mollusk shells are among biomaterial nanocomposites that their layered structures are composed of organic and inorganic materials. Since the nanoindentation process is known as an efficient method to determine mechanical properties like elastic modulus and hardness in small scale, therefore, due to some limitations of considering all peripheral parameters, particular simulations of temperature effect in the atomic scale are considerable. The present article provides a molecular dynamics approach for modeling the nanoindentation mechanism with three types of pyramidal, cubic, and spherical indenters at different temperatures of 173, 273, 300, and 373°K. Based on load-indentation depth diagrams and Oliver–Pharr equations, research findings indicate that the temperature has weakened the power between the biological atoms; this leads to reduced mechanical properties. An increase in temperature causes a reduction in elastic modulus and hardness. There was correspondence between the results obtained from the spherical indenter and experimental data. This study can be regarded as a novel benchmark study for further research studies which tend to consider structural responses of the various bio-inspired nanocomposites.