The binding geometries, abilities and thermodynamic parameters for the intermolecular complexation of two water-soluble calixarenes, p-sulfonatocalix[4]arene (SC4A) and p-sulfonatocalix[5]arene (SC5A), with biguanidinium guests, metformin (MFM) and phenformin (PFM), were investigated by (1)H and 2D NMR spectroscopy, X-ray crystallography, and isothermal titration calorimetry (ITC). The obtained results show that biguanidinium guests are captured by calixarenes with the alkyl or aromatic portion immersed into the cavities and the guanidinium portion fixed at the upper-rims. At both acidic and neutral conditions, SC4A always presents stronger binding affinities to biguanidinium guests than SC5A. Moreover, SC4A prefers to include MFM rather than PFM. As a result, the binding selectivity of MFM is up to 44.7 times for the SC4A/SC5A hosts. The intrinsic relationship between binding structures and selectivities were comprehensively analyzed and discussed from the viewpoint of thermodynamics. Finally, the ITC measurements were further performed in phosphate buffer instead of aqueous solution, to examine the buffer effects, counterion effect, and the differences between thermodynamic and apparent association constants.