In this study, a butadiene-isoprene coordination polymerization was initiated by a binary molybdenum (Mo)-based catalytic system consisting of modified MoO2Cl2 as the primary catalyst, triethyl aluminum substituted by m-cresol as the co-catalyst and tris(nonyl phenyl) phosphate (TNPP) as the ligand. The effects of the amount of catalyst and type of co-catalyst were investigated in detail. Experimental results indicated that when the butadiene-isoprene coordination polymerization was initiated by the binary Mo-based catalytic system, the monomer conversion could reach 90%. The resulting butadiene units were primarily based on 1,2-structures, and the reactivity ratios of butadiene and isoprene were 1.13 and 0.31, respectively. The reaction in the catalytic system was attributed to the non-ideal and non-constant ratio copolymerization. When the addition of isoprene monomers was relatively low, the isoprene units on the butadiene-isoprene copolymers were primarily based on the 1,2- and 3,4-structures. Moreover, the orientation of active centers to 1,2- and 3,4-structures gradually decreased with an increase in the addition of isoprene monomers, which resulted in the generation of high vinyl butadiene-isoprene copolymers.