In this research, the effect of the atomic radius of silica nanoparticles (SiO2) on the tensile and thermal properties of polylactic acid (PLA) based nanocomposites was analyzed. Different nanocomposite samples were made using PLA matrix with three atomic radius ranges of 15–20 nm, 20–30 nm, and 50–70 nm, and three-volume percentages (1, 2, and 3%) SiO2 nanoparticles. First, to observe the state of dispersion of SiO2 nanoparticles in the fabricated samples, photographs were taken with the field emission scanning electron microscope (FESEM) and the platinum coating method. FESEM images showed that 15–20 nm and 20–30 nm nanoparticles were better dispersed in the PLA matrix than 50–70 nm due to their smaller size. Then experimental tests were performed on the samples and parameters of modulus of elasticity, tensile strength, and heat deflection temperature (HDT) were measured. The results of the experiments showed that 15–20 nm SiO2 nanoparticles caused a 1% decrease in modulus of elasticity, a 2% decrease in tensile strength, and a 3.5% increase in HDT temperature. 20–30 nm SiO2 nanoparticles increased the modulus of elasticity by 8.8%, tensile strength by 1.8%, and HDT temperature by 1%. 50–70 nm SiO2 nanoparticles also caused a 3.3% increase in modulus of elasticity, a 1.1% increase in tensile strength, and a 4% increase in HDT temperature. The results showed that besides the volume fraction, the size of the reinforcing nanoparticles is also an effective factor in the mechanical properties of PLA nanocomposites.