It was found that self-lignment of hemicyanine molecules existed in the unpoled hemicyanine doped silica film fabricated by sol-gel technique. A χ(2) value of 6.6 pm/V was obtained for a 50 nm thick film. Time evolution of hemicyanine structural changes and their influence on second order nonlinearity were investigated. It was found that transfer of protonated hemicyanine to monomeric and aggregated hemicyanine occurred within 4 hours after film deposition, during this period of time SHG signal continued to rise and reached maximum final1y. Blue shifting of both aggregate and monomer absorption peaks were found accompanied with the drying of the film.