The invention provides a waste treatment system as well as a treatment method and application thereof. The system comprises a piece of hydrothermal treatment equipment, a first solid-liquid separating mechanism, a piece of aeration treatment equipment and a piece of anaerobic digestion equipment, wherein the hydrothermal treatment equipment comprises a hydrothermal treatment device; the material is liquefied by steam filling into the hydrothermal treatment device to obtain a liquefied product; the first solid-liquid separating mechanism is used for dividing the liquefied product into a first liquid material and a first residual material; the aeration treatment equipment is used for aerating the first liquid material and removing heavy metals in the first liquid material to obtain a second liquid material; the anaerobic digestion equipment comprises a digestion treatment device; inoculated sludge conveyed to the digestion treatment device is used for carrying out anaerobic digestion treatment on the second liquid material to obtain anaerobic digestion gas and discharge digestion liquid. Due to the adoption of hydrothermal treatment, the loss of the thermal energy is reduced; then the aeration treatment equipment is used for removing the heavy metals and other harmful substances in the first liquid material; then the anaerobic digestion treatment is carried out, so that the anaerobic digestion treatment is relatively easy to operate.