Recently, there has been an increasing interest in liquid rubbers (LRs), which can work as reactive processing aids to replace conventional plasticizers and are used as prepolymers to synthesize novel block copolymers. However, the understanding of effects of their microstructures on the properties of materials is still not sufficient. In this study, liquid 1,4-polyisoprene (L1,4-IR) and liquid 3,4-polyisoprene (L3,4-IR) with similar molecular weight were selected and mixed with styrene-butadiene rubber (SBR)/butadiene rubber (BR). The effects of microstructures of the LRs on the properties of materials were investigated. L1,4-IR has more 1,4-units and fewer 3,4-units than L3,4-IR. This gives L1,4-IR a lower glass transition temperature and much more flexible polymer chains. Vulcanizates containing L1,4-IR had advantages over samples containing L3,4-IR, including lower Mooney viscosities, smaller ΔG 0 value from 0.3% to 43% of strain, fewer sol fractions, better abrasion resistance and lower values of tan ⊐ at 60 °C. In contrast, high contents of 3,4-units endow L3,4-IR with low unsaturation in polymer backbones and high glass transition temperature. Samples containing L3,4-IR showed higher values of tan ⊐ at 0 °C, better thermal stabilities and excellent DIN abrasion resistance after aging compared to samples with L1,4-IR. Furthermore, there were no big differences in the mechanical properties of SBR/BR compounds containing L1,4-IR or L3,4-IR. The results of this study are of great importance to the practical application of liquid polyisoprene in the rubber industry.