Shear alignment behavior was examined for smectic CA (SCA) phase of main-chain BB-5(3-Me) polyester using a cone-and-plate fixture. In the smectic temperature region from 100 to 140 °C, two distinct orientations have been identified by wide-angle X-ray diffraction. At temperatures lower than 130 °C, the smectic layers arrange with unit normal perpendicular to the shear direction and parallel to the velocity gradient direction (so-called parallel orientation). Shearing at high temperatures near the isotropization temperature leads to the orientation of smectic layers with unit normal perpendicular to both the flow and velocity gradient directions (perpendicular orientation). At the intermediate temperatures, both orientations coexist. The SR-SAXS profile of the parallel oriented sample measured with irradiation along the vorticity direction includes a small peak with a spacing of around 80 Å in the velocity gradient direction that is parallel to the chain axis. The long spacing is roughly 5 times larger than the length of repeat unit, i.e., the smectic layer thickness (16.4 Å), showing the existence of chain-folded lamellae. The parallel orientation is attributed to mutual slide of the chain-folded lamellae. At higher smectic temperatures, on the other hand, the flow of the molecules within a smectic layer takes place preferentially to the mutual slide of lamellae, which is responsible for perpendicular orientation.