The microlamellar and smectic liquid crystal (LC) structures in a block copolymer of a main-chain LC polyester with poly(ethyl methacrylate) at each end are investigated by fiber X-ray scattering. In the as-spun fiber, the lamellae are parallel to the fiber axis, while the smectic layers are perpendicular to it. Annealing the as-spun fiber at a temperature higher than the isotropization temperature (Ti) of the LC segment, the lamellae are preserved, but the LC structure disappears. Further annealing the fiber at T < Ti improves the lamellar stacking coherence and aligns the smectic layers parallel to the lamellae. In contrast, annealing the as-spun fiber at T < Ti conserves the smectic layers and arranges the lamellae in parallel to the smectic layers. Thus, the liquid crystallinity affects the lamellar ordering and orientation.