Abstract: With femtosecond laser pulse shaping technique, the coherent control of non-resonant two-photon transition in a molecular system (perylene dissolved in chloroform solution) is studied theoretically and experimentally. The femtosecond pulse is shaped with simple phase patterns (cosinusoidal and phase step-function shapes) and it is found that the two-photon transition probability in molecular systems can be reduced but cannot be eliminated. Coherent control of non-resonant two-photon transition in a molecular system is correlated with both the laser field and the molecular absorption bandwidth. In contrast with atomic system, control efficiency of two-photon transition in molecular systems is reduced.