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This paper studies the mode choice problem considering the peak travel chain in a day. The transportation system comprises a subway parallel to a bottleneck-constrained highway between a residential area and a working place. Commuters can get their destinations by either auto or transit only; besides these two modes, they can drive to .the bottleneck, park there and then take subway to the destination. Based on the bottleneck theory, a hierarchical Logit model is used to describe commuters' mode choice behaviors, and then mode choice equilibrium equations under elastic demand are constructed. Furthermore, optimal fare and parking fee strategies under four mechanisms are discussed. It is shown that when transit and park-and-ride place are operated by government and the working area parking lot belongs to a private enterprise, lower fares and higher parking fees in working area can effectively encourage parking interchanging, increase public transit trip contribution rate and maximize the system's total net benefit. Numerical results also support the current differentiation parking charge policy in Beijing. [ABSTRACT FROM AUTHOR]