We demonstrate a new and simple method of precisely fabricating defects in three-dimensional (3D) CdS macroporous photonic crystals (PCs) with a variable pressure scanning electron microscope. Well-defined point defects, not only vacancies but also an impurity (a reduced-size sphere), were directly fabricated by electron-beam irradiation under a gas atmosphere. This provides a convenient and straightforward method of introducing various designed defects into 3D PCs for photonic-band-gap-based applications.