A living tissue bonding system includes a treatment instrument having a heating element which applies thermal energy to living tissue, an element temperature measuring section configured to measure an element temperature T1 of the heating element, a power source configured to generate power, a first calculating section configured to estimate a temperature difference ΔT between the element temperature T1 and a temperature T2 of the living tissue using a table or an equation stored beforehand in order to estimate the temperature difference ΔT based on an output value of the power source, a second calculating section configured to estimate the tissue temperature T2 from the element temperature T1 and the temperature difference ΔT estimated by the first calculating section, and a control section configured to control the power source based on the tissue temperature T2 estimated by the second calculating section.