According to the multi-project and program management theory, this paper analyzes the program generation principle and establishes a program based on progress goals. On the basis of the present situation of calculation of penalty for delay of the bidding section construction period with the critical path method, we studied the effects of contractor-induced delay of the bidding section construction period in detail, including the effects on the construction period of the bidding section itself, the earliest start times of the next bidding section and other subsequent bidding sections, and the construction period of the program, and then constructed a penalty model for delay of the bidding section construction period from the perspective of programs. Using the penalty model, we conducted a practical analysis of penalty for delay of the construction period of the Baoying station program in the South-to-North Water Diversion Project. The model can help determine the amount of penalty for delay of the construction period in bidding sections scientifically and reasonably.