The invention discloses a shale reservoir free gas content earthquake predicating method and a system thereof. The method comprises the steps of respectively acquiring work area elastic parameters andtime domain well logging data based on a work area pre-stack seismic data volume and depth domain well logging data; establishing a rock physical model based on the work area elastic parameters, andobtaining porosity and gas saturation; based on seismic data and ground temperature gradient, respectively acquiring a stratum pressure and a stratum temperature, and furthermore obtaining a volume coefficient; and based on the porosity, the gas saturation, the volume coefficient and the stratum pressure, establishing a calculation model of the free gas content, thereby obtaining the free gas content, wherein the work area elastic parameters comprise longitudinal wave impedance, transverse wave impedance and density. According to the shale reservoir free gas content earthquake predicating method and the system, through restraining the factors such as the stratum temperature, the stratum pressure, porosity and gas saturation, high-precision predication for free gas content of the shale reservoir is realized.