This study examined crystal orientation confined within a lamellar microdomain morphology formed by the blends of polystyrene-block-poly(ethylene oxide) (PS-b-PEO) and polystyrene-block-poly(acrylic acid) (PS-b-PAA) through wide-angle X-ray diffraction. The hydrogen-bonding interaction between PEO and PAA molecules enabled block copolymers to co-organize into a microphase-separated morphology without inducing macrophase separation, but it hampered PEO crystallization. PEO crystallization that occurred at −20 °C resulted in the nucleation mechanism to be dominant, thus leading to the formation of small crystals. Small crystals allowed them to be free from spatial confinement, and they tended to be oriented with their c-axis parallel to the microdomain interface. By contrast, when PEO was crystallized at 40 °C, the high temperature facilitated PEO crystals to exhibit large crystallite sizes, which aligned perpendicularly to the microdomain interface. An increase in the PS-b-PAA concentration considerably reduced the crystallizability of PEO. The presence of a low amount of crystals and additional lateral confinement formed by hydrogen-bonded PEO/PAA reduced the degree of orientation regardless of the crystallization temperature.