In this paper, the synthesis and magnetic properties of mononuclear Fe-containing polyoxometalates (POMs) with different types of heteroatoms, TBAH[(A-α-XWO)Fe] (II, X = Ge, Si; TBA = tetra- n-butylammonium), are reported. In these POMs, mononuclear highly distorted six-coordinate octahedral [FeO] units are sandwiched by two trivacant lacunary units [A-α-XWO] (X = Ge, Si). These POMs exhibit field-induced slow magnetic relaxation based on the single high-spin Fe magnetic center ( S = 5/2). Combining experiment and ab initio calculations, we investigated the effect of heteroatoms of the lacunary units on the field-induced slow magnetic relaxation of these POMs. By changing the heteroatoms from Si (II) to Ge (II), the coordination geometry around the Fe ion is mildly changed. Concretely, the axial Fe-O bond length in II is shortened compared with that in II, and consequently the distortion of the [FeO] unit in II from the ideal octahedral coordination geometry becomes larger than that in II. The effective demagnetization barrier of II (11.4 K) is slightly larger than that of II (9.2 K). Multireference ab initio calculations predict zero-field splitting parameters in good agreement with experiment. Although the differences in the coordination geometries and magnetic properties of II and II are quite small, ab initio calculations indicate subtle changes in the magnetic anisotropy which are in line with the observed magnetic relaxation properties.