In order to understand the trans-1,4 stereospecific polymerization mechanism of conjugated dienes with the heterogeneous Ziegler-Natta catalyst, isoprene polymerization kinetics at different polymerization temperature in the initial polymerization stage and the microstructures of polymers and its fractions were studied in this work. Both polymerization temperature and time influenced the polymerization behavior greatly. The nascent polyisoprene (30s) with unusual high cis-1,4-units was observed and then the trans-1,4/cis-1,4 ratio of the polymers increased obviously to finally trans-1,4-dominated (96 mol%) with the increase in polymerization time. Fractions of the products based on the different crystallizability at different temperature were isolated and characterized by 1H-NMR, 13C-NMR, GPC and DSC. The nascent polyisoprene under 30s polymerization time was mainly composed by fractions A and G with 30–60 mol% trans-1,4-units and 2–26 mol % trans-cis dyad linkages. Active species with low stereoregularity may contribute to theses fractions. While fractions D and E with high trans-1,4 unit (>96 mol%) from active species with high stereoregularity were growing to the predominated components with increased conversion. At least two kinds of active species with different stereospecificity and lifetime were proposed to explain the isoprene polymerization with heterogeneous TiCl4/MgCl2-Al(i-Bu)3 catalyst. Effects of temperature on cis/trans-1,4 structure were discussed. Hopely, this research would provide a further understanding about trans-1,4 stereospecific polymerization of conjugated dienes with heterogeneous Ziegler-Natta type catalysts.