The frustules of diatoms have excellent elasticity and high strength, but their main composition, amorphous silica, is a kind of typical brittle material. Molecular dynamics simulations of the uniaxial tension were carried out to study the size effect on the mechanical properties of amorphous silica. Stress-strain behavior, the radius of biggest void, radial distribution functions and bond angle distribution were analyzed. Our results show the small model exhibits a better ultimate strength, ductility and toughness than the large model, and the generation and expansion of voids plays an important role in the fracture behavior of the model. For the small model, some of Si-O bonds are stretched, and the average of O-Si-O bond angle decreases from 108 degrees to 95 degrees, which makes the model have a capability to perform larger plastic deformation and lead to a better ductility. However, for the large model, except the change of Si-O-Si bond angle, its structure has no other significant changes. Our results demonstrate that changes of size have significant impact on the mechanical properties and deformation mechanism of intrinsically brittle materials at the nano-scale.