The deformation behavior of polythiourethane (PTU) elastomers was investigated using in situ small-angle X-ray scattering (SAXS), wide-angle X-ray diffraction (WAXD), and X-ray absorption fine structure (XAFS) methods. Two PTUs were prepared from poly(oxytetramethylene) glycol, 1,4-bis(isocyanatomethyl) cyclohexane, and 1,4-butanedithiol (PTU-B) or 1,5-pentanedithiol (PTU-P). The effect of methylene length of the chain extender on molecular aggregation structure of PTU during the elongation process was evaluated. SAXS measurement revealed that the spacing of hard segment domains of PTUs increased and decreased in the directions parallel and perpendicular to the elongation direction and showed a constant value of strain above 2. The strain calculated from the spacing of the hard segment domains for PTU-B was larger than that for PTU-P, suggesting that well-developed hard segment domains were formed for PTU-B. WAXD measurement showed that strain-induced crystallization of the soft segment occurred at around the strain of 2. XAFS measurement showed that at the strain of 2 or 3, atoms in the vicinity of sulfur became more ordered, which is confirmed by the decrement of the extended XAFS Debye-Waller factor. It seems reasonable from these SAXS, WAXD, and XAFS results that the hard segment domains orientation occurred for both PTUs during the deformation process, followed by strain-induced crystallization of the soft segment. In addition, PTU-B exhibits more ordered hard segment domains that maintain their aggregation structure upon uniaxial deformation in comparison with PTU-P.