A novel series of morpholinium salts, N-alkyl-N-methylmorpholinium salts (Mor(1,n)X, n=10, 12, 14, 16, X=BF4-) and Bronsted acidic N-hexadecyl morpholinium salts (Mor(16)X, X=BF4-, CH3SO3- and p-CH3C6H4SO3-) were synthesized. And their mesomorphic properties were characterized by differential scanning calorimetry and polarized optical microscopy. The single crystal X-ray diffraction and the detailed temperature dependent small angle X-ray diffraction were used to investigate the molecular structure of Mor(1,16)BF(4). These results suggested that the BF4- favor the formation and stabilization of mesogenic compounds. And hydrogen bonds between the BF4- and morpholinium cations contributed to the conformational change of phase transition of Mor(1,16)BF(4)(.)