A junction structure and a joining method of substrates are provided that stably can join the substrates and achieve high workability during joining. A second substrate 2 to be joined with solder to a first substrate 1 is bent with elasticity generated by a bending portion 9, and first joints 5 on the first substrate 1 and second joints 6 on the second substrate 2 are joined with solder in a state in which the first substrate 1 is brought into contact with, in a direction that increases the bending angle of the bending portion 9, a part where the joints 6 are formed on the second substrate 2.