The nano‐size autonomous monodisperse silica (AS) particles were prepared by hydrolysis and condensation of tetraethoxysilane using l‐lysine as catalyst. The silica/natural rubber (NR) masterbatches were then produced via latex compounding, in which NR latex was mixed with the above AS dispersion. The commercial precipitated silica (PS) was introduced as a control. The effects of both AS and PS particles on the interfacial and mechanical properties of composites were systematically examined. It was found that the AS formed bead‐like morphology wherein the clear particle edges can be distinguished in rubber matrix. Compared with PS/NR, the AS/NR composites were proved to possess more bound rubber and weaker filler–filler interaction resulting in higher tensile strength, abrasive resistance, and resilience. Meanwhile, the efficiency of premodified AS and PS surfaces using bis‐(3‐triethoxysilylpropyl) tetrasulfide on reinforcing the properties of silica/NR composites was studied. The results presented that the overall properties of modified silica/NR vulcanizates were improved significantly. In special, the values of heating building‐up and compression set showed an evident decline which was of great significance for tire tread or other rubber products. For the dynamic properties, the magic angle spinning/NR composites had lower rolling resistance. In short, AS may be applied as an ideal substitution of PS in rubber. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47449.