The invention discloses a method and system for determining a shale natural gas advantageous reservation mode. The method comprises the following steps that: the equal free adsorption critical porosity of a shale gas reservoir is determined by using logging data; the effective porosity of the shale gas reservoir is determined by using the logging data; and the shale natural gas advantageous reservation mode is determined according to the equal free adsorption critical porosity and the effective porosity. With the method and system of the invention adopted, a convenient means is provided for the determination of the shale natural gas advantageous reservation mode. The method and system have a great practical value in shale gas exploration and development.