A flexible interlocking structure for a handheld endoscope includes a flexible rod having an interlocking unit connected to its one end. The interlocking unit includes front, middle and rear joints each having a hollow portion. Each joint is formed with at least two guiding holes, locking tabs and locking notches. The engagement between the locking tabs and the locking notches of the adjacent joints constitutes the interlocking unit. Both ends of the flexible rod are connected to a handle portion and an inspection module respectively. A transmission cable and driving wires are disposed through the hollow portions and the guiding holes in such a manner that they are located between the inspection module and the handle portion. By operating a steering device of the handle portion, the driving wires pulls the front joints to cause the interlocking unit to bend accordingly, thereby controlling the rotation of the inspection module.