A series of iminopyridine complexes of Fe(II) and Co(II) complexes bearing fluorinated aryl substituents were synthesized for the polymerization of isoprene. The structures of complexes 3a, 2b and 3b were determined by X-ray diffraction analysis. Complex 3a contained two iminopyridine ligands coordinated to the iron metal center forming an octahedral geometry, whereas 2b adopted a chloro-bridged dimer, and 3b featured with two patterns of cobalt centers bridged via chlorine atoms. Complexes 2b and 3b represented rare examples of chlorine bridged bimetallic Co(II) complexes. The fluorine substituents effects, particularly on catalytic activity and polymer properties such as molecular weight and regio-/stereo-selectivity were investigated when these complexes were employed for isoprene polymerization. Among the Fe(II)/methylaluminoxane (MAO) systems, the 4-CF3 substituted iminopyridine Fe(II) complex 1a was found as a highly active isoprene polymerization catalyst exhibiting the highest activity of 106 g·(mol of Fe)−1·h−1. The resultant polymer displayed lower molecular weight (Mn = 3.5 × 104 g/mol) and moderate polydispersity index (PDI = 2.1). Furthermore, the ratio of cis-1,4-/3,4 was not affected by the F substituents. In the series of Co(II)/AlEt2Cl binary systems, complexes containing electron-withdrawing N-aryl substituents (R = 4-CF3, 2,6-2F) afforded higher molecular weights polyisoprene than that was obtained by the complex containing electron-donating N-alkyl substituents (R = octyl). However, ternary components system, complex/MAO/[Ph3C][B(C6F5)4] resulted in low molecular weight polyisoprene (Mn < 2000) with high trans-1,4-unit (>95%).