Three α-Keggin heteropolymolybdates with the formula [(C5H4NH)COOH]3[PMo12O40] 1, {[Sm(H2O)4(pdc)]3}{[Sm(H2O)3(pdc)]}[SiMo12O40]·3H2O 2 and {[La(H2O)4(pdc)]4}[PMo12O40]F 3 (H2pdc = pyridine-2,6-dicarboxylate), have been synthesized under hydrothermal condition and characterized by single crystal X-ray diffraction analyses, elemental analyses, inductively coupled plasma atomic emission spectroscopy (ICP-AES), IR, thermal gravimetric analyses, thermal infrared spectrum analyses and powder X-ray diffraction (PXRD) analyses. Single crystal X-ray diffraction indicates all three compounds comprise ball-shaped Keggin type [XMo12O40]n− polyoxometalates (POMs) (n = 3, X = P; n = 4, X = Si, respectively) with different types of carboxylic ligands derived from H2pdc, and these cluster anions are isostructural. In order to explore structural characteristics, Rhodamine B photocatalytic (RhB) degradation and two-dimensional infrared correlation spectroscopy (2D-IR COS) tests, are investigated for 1, 2 and 3. In RhB degradation, all compounds show good photocatalytic activity. For 1, the activity mainly comes from POMs. While in 2 and 3, POMs’ photocatalytic activity is enhanced by the Ln(III)–pdc metal–organic frameworks. Structural properties like POM's stability and magnetic sensitivity are discussed by 2D-IR COS under thermal/magnetic perturbations.