In this work, we have synthesized four SAPO-34/44 (framework type code: CHA) samples by utilizing different organic structure-directing agent (OSDA) such as cyclohexylamine (CA), n-butylamine (BA), diisopropylamine (DIPA), and dipropylamine (DPA). An approach combining Rietveld refinement and simulated annealing has been successfully applied to determine the location of the individual OSDA and the host (inorganic framework)-guest (OSDA) interaction. The final Rietveld refinements show that 1) one cha cage can be occupied by either two OSDAs (CA and BA) in the up-and-down arrangement or one OSDA (DIPA and DPA) in the longitudinal configuration and 2) the classical hydrogen bond between CA/BA and the inorganic framework in SAPO-44-CA and SAPO-34-BA could be identified. The host-guest interactions among these four samples are also investigated by FT-IR, which are consistent with Rietveld refinement results. The approach employed here could be applicable for the host-guest investigation in other crystalline porous materials.