Three indole-based nonlinear optical (NLO) chromophores with changeable isolation groups were successfully introduced into the polymer backbone to yield a series of main-chain polyurethanes. Thanks to the main-chain structure and the advantages of the indole-based chromophores, all of the polymers show excellent transparency, good processability, thermal stability, and relatively good NLO effects. The obtained experimental results indicated that the polymer backbone, in addition to the linked isolation moieties, could act as isolation spacers in some special cases. The tested NLO results demonstrated that the isolation groups with apparent site-isolation effect might not benefit the macroscopic NLO effect of the resultant polymers.