To access smart optical theragnosis for cancer, an easily processable heterocyclic conjugated polymer (poly(sodium3-((3-methyl-3,4-dihydro-2H-thieno[3,4-b][1,4] dioxepin-3-yl) methoxy) propane-1-sulfonate), PPDS) nanoassembly is fabricated by a surfactant-free one-step process, without the laborious ordinary multicoating process. The conjugated nanoassembly, with a self-doped structure, provides strong absorbance in the near-infrared (NIR) range even in a neutral pH medium and exhibits excellent stability (>six months). In addition, the prepared PPDS nanoassembly shows a high photothermal conversion efficiency of 31.4% in organic photothermal nanoparticles. In particular, the PPDS nanoassembly is stably suspended in the biological medium without any additives. Through a simple immobilization with the anti-CD44 antibody, the prepared biomarker-targetable PPDS nanoassembly demonstrates specific targeting toward CD44 (expressed in stem-like cancer cells), allowing NIR absorbance imaging and the efficient targeted photothermal damaging of CD44-expressing cancer cells, from in vitro 3D mammospheres (similar to the practical structure of tumor in the body) to in vivo xenograft mice tumor models (breast cancer and fibrosarcoma). In this study, the most simplified preparation method is for this organic conjugated polymer-based nanoassembly by a molecular approach is reported, and demonstrated as a highly promising optical nanoagent for optical cancer theragnosis.