Chemical cross-linking was introduced to enhance the mechanical and thermal properties of thermoplasic elastomer, i.e., polyurethane. By changing the amount of cross-linking agent added, cross-linking density was controlled and relationship between the internal structure and mechanical properties has been studied. Polyurethane used in this study consists o 4, 4'-diphenyl-methane diisocyanate (MDI), 1, 4-butanediol as a hard segment and polytetramethylene glycol (PTMG MW=1000 g/mol) as a soft segment. Cross-linking agent having free isocyanate functional groups at both chain ends was prepared with PTMG (MW=1000 g/mol) end-capped with MDI. By melt-blending the polyurethane with cross-linking agent in an extruder at 200℃∼220℃, allophanate functional groups were expected to form through chemical reaction between the N-H group in the hard segment and free isocyanate group in the cross-linking agent. Four samples having 0%, 10%, 15%, 20% (w/w) cross-linking agent were prepared. From stress-strain curve, the mechanical properties and hysteresis behavior of four samples were evaluated. And the effect of cross-linking on the degree of phase separation was studied with the DSC and FTIR-ATR measurements. Using synchrotron small angle X-ray scattering method, thermal stability of hard domain was investigated. upon cross-linking, mechanical properties were observed to be enhanced, however, the thermal stability was lowered.