Spontaneous chain polymerization of molecules initiated by a scanning tunneling microscope tip is studied with a focus on its rate-determining factors. Such chain polymerization that happens in self-assembled monolayers (SAM) of diacetylene compound molecules, which results in a π-conjugated linear polydiacetylene nanowire, varies in its rate P depending on domains in the SAM and substrate materials. While the arrangement of diacetylene molecules is identical in every domain on a graphite substrate, it varies in different domains on a MoS(2) substrate. This structural variation enables us to investigate how P is affected by molecular geometry. An important determining factor of P is the distance between two carbon atoms which are to be bound by polymerization reaction, R; as R decreases by 0.1 nm, P increases ∼2 times. P for a MoS(2) substrate is ∼4 times higher (with the same value of R) than that for a graphite substrate because of higher mobility of molecules. The exciting correlation of the chain polymerization rate to the geometrical structure of the diacetylene molecules brings a deeper understanding of the mechanism of chain polymerization kinetics. In addition, the fabrication of one-dimensional conjugated polymer nanowires on a semiconducting MoS(2) substrate as demonstrated here may be of immense importance in the realization of future molecular devices.