A femtosecond laser pulse can be tailored to control the two-photon transitions using the ultra-fast pulse-shaping technique. This paper theoretically and experimentally demonstrates that two-photon transitions in molecular system with broad absorption line can be effectively controlled by square phase-modulation in frequency domain, and the influ-ence of all parameters characterizing the square phase-modulation on two-photon transitions is systemically investigated and discussed. The obtained results have potential application in nonlinear spectroscopy and molecular physics.