An earlier proposed strategy to orient two merocyanine dyes in the desirable head-to-tail parallel fashion through multiple hydrogen bonds has been examined by molecular dynamics simulations and quantum chemical calculations. Two different merocyanine dyes dissolved in chloroform solution under various conditions are simulated by molecular dynamics. It is found that two dipolar units can be well connected through various numbers of hydrogen bonds. Although the probability to form the desirable head-to-tail dimer is unfortunately small even under strong poling electric field and low temperature, the formation of unwanted antiparallel structure has been effectively reduced. Typical hydrogen bonded dimers obtained from molecular dynamics simulations have been studied by hybrid density functional calculations. It is found that only the most probable complex can lead to the optical absorption spectrum that is in close agreement with the corresponding experiments. Calculated results for dipole moments of ground and charge transfer states, as well as first hyperpolarizabilities, of three typical complexes have also been provided.