We propose the question of the modulated structures of copper oxide is caused by the [CuO2] in‐plane oxygen vacancy or apical oxygen vacancy. Sr2CuO3+δ single‐crystal samples were prepared using high‐temperature and high‐pressure methods. The major phase of Sr2CuO3+δ (δ = 0.4) single‐crystal system is found to be constituted by the 52 a modulated structure with the Fmmm space group, which originates from the [CuO2] in‐plane oxygen vacancy appearing in octahedral Cu‐O. Besides, the presence of the [CuO2] in‐plane oxygen vacancy may obliterate the superconductivity of the system. Experimental results deduce that the oxygen vacancy may appear in the apical oxygen sites in high‐temperature copper oxide superconductors.