It is known that lysophospholipids (LPLs) may affect rice starch pasting and thermal properties possibly through the formation of an amylose-lipid complex. However, whether these effects of rice LPLs are independent of amylose are still not understood. Here, the diversity of rice flour pasting and thermal properties and their relationship with individual LPL components in native rice endosperm were studied. Several significant correlations between LPLs and pasting properties, such as cool paste viscosity (CPV), breakdown (BD) and consistency (CS) were clearly evident. Thermal properties generally had no relationship with LPLs except for gelatinization enthalpy. Using partial correlation analysis we found that, irrespective of apparent amylose content, CPV and individual LPLs were positively correlated, while BD, CS and other individual LPLs were negatively correlated. This study suggests naturally occurring individual LPLs can contribute to rice flour pasting and thermal properties, either independently or in combination with amylose.