Three polymeric heterothiometallic clusters with 3D pillar-layer-alternating honeycomblike frameworks are synthesized by a one-pot self-assembly reaction. Z-scan experiments demonstrate that the nonlinear optical (NLO) behavior of these clusters can be modulated by modifying the conjugated chain of the connecting backbone ligands (see figure). Time-dependent density functional theory calculations support and rationalize the observed NLO modulation.