Based on the particularity of underwater concrete structure, a temperature tracer method based on heat transfer theory for crack detection was proposed. The basic way to identify cracks is to change the thermodynamic boundary conditions around cracks after cracking, which will lead to the change of cooling rate of the heat source near cracks. Based on this idea, a set of crack monitoring system composed of a temperature sensing system, a heating system, a monitoring tube and multiple casing tubes was designed. By using this system, a series of crack monitoring tests were carried out on two kinds of concrete specimens. The results show that the monitoring scheme with casing tube can detect the crack position in still water, and this monitoring scheme can detect both crack position and width in flowing water. The sensitivity of it is higher than that of the monitoring scheme without casing tube.