The present application provides a method and a system for determining a saturation exponent of a heterogeneous carbonate reservoir. The method comprises: dividing a target reservoir into at least two reservoir types in accordance with a predetermined rule; obtaining a correspondence relationship between a saturation exponent and a bound water saturation in each of the reservoir types; determining the reservoir type to which a to-be-measured core belongs in accordance with the predetermined rule; obtaining a bound water saturation of the to-be-measured core; and calculating the saturation exponent of the to-be-measured core according to the bound water saturation of the to-be-measured core on the basis of the correspondence relationship of the reservoir type to which the to-be-measured core belongs.