Changes in the microphase-separated structure of the poly(styrene-b-ethylene-co-butylene-b-styrene) (SEBS) triblock copolymer (13 wt % polystyrene (PS) block) were investigated during mechanical deformation. In situ synchrotron radiation small-angle X-ray scattering (SAXS)/wide-angle X-ray scattering (WAXS) measurements were successfully performed for SEBS under equi-biaxial deformation as well as under uniaxial deformation. In situ SAXS/WAXS measurements revealed changes in (1) the shape of spherical PS domains, (2) the spacing of PS domains packed in the body-centered cubic structure in the initial state, (3) their ordering, and (4) the orientation of PEB chains during deformations. In terms of the microdomain structure, affine deformation was kept below a certain strain (epsilon(d-A)), which are 4 and 1.2 for uniaxial and equi-biaxial deformation, respectively. In contrast, the ordering of the arranged PS domains decreased from the initial strain region. Above the epsilon(d-A) value, deviation from affine deformation started to occur. This deviation is related to contact of PS domains under mechanical deformation. Uniaxial stretching still showed the plane-independent behavior, while equi-biaxial stretching did not. Moreover, the epsilon(d-A) value for equi-biaxial deformation was smaller than that for uniaxial deformation and further smaller than expected. This might be because the entanglement effect was enhanced for equi-biaxial deformation. Furthermore, after contact of PS domains at around strains of 6 and 2, during uniaxial and equi-biaxial deformation, respectively, the ordering of PS domains suddenly increased with an increase in strain. It is inferred that the locked state between the PS domains and the extended PEB chains formed during deformation may have been released and repacked at a certain strain.