The shear flow orientation in the diblock copolymers composed of polystyrene (PS) and side-chain liquid crystal polymer (LCP) was investigated by the wide and small-angle X-ray diffraction methods. Two diblock copolymers prepared by atom transfer radical polymerization have the weight fractions of the PS segment of 0.13 and 0.21, and form a well-defined microsegregation structure with PS cylinders hexagonally packed in a matrix of LCP which forms smectic A, nematic, and isotropic phases in order of increasing temperature. Two types of shear flow orientation have been observed, depending on the type of the phase in the LCP matrix. The shear flow at nernatic temperatures orients well the PS microcylinders as well as the LC mesogens in the velocity direction. This parallel-b orientation is expectable from the general orientation of the microcylinders and the LC mesogens in shear flow. When the LCP matrix transforms to the smectic LC, the mesogens are aligned parallel to the velocity gradient direction entailing significant disturbance for the microcylinders. By annealing this sample at nernatic temperature, a well-defined perpendicular-c orientation can be attained with both the microcylinders and the mesogens lying parallel to the velocity gradient direction. These two characteristic orientations can arise from compromises between the orientations of the microcylinders and the LC mesogens.