For the first time, the indole-based NLO chromophores were embedded into the polymer main chain, and different isolation groups were attached to their donor side with the efforts of adjusting the NLO properties of the resultant main-chain polyurethanes, according to the site isolation principle. Thanks to the main-chain structure and the advantages of the indole-based chromophores, all the polymers show excellent transparency, good processability, thermal stability, and relatively good NLO effects. The tested NLO properties of the polymers demonstrate that there is a suitable isolation group present for the sulfonyl-based chromophore to boost its microscopic beta value to a possibly higher macroscopic NLO property efficiently.