We have investigated the structure of the mixed Langmuir-Blodgett (LB) film of a merocyanine dye derivative (MO(18))-deuterated arachidic acid (C(20)-d) binary system and the influence of successive hydrothermal treatment in the liquid phase (HTTL) on the mixed LB film by means of polarized UV-visible and IR absorption spectroscopy. The visible absorption band with in-plane anisotropy at 503 nm before HTTL transforms into an absorption band with in-plane isotropy at 557 nm after HTTL for 16-18 min through a peak maximum near 520 nm after HTTL for 2-12 min. The degree of total MO(18) intramolecular charge transfer for the 503 nm band is the largest among those for all of the bands. Therefore, the 503 nm band is ascribed to the MO(18) H-like aggregation, based on its shape, peak height, and in-plane anisotropy, the subsequent change to two kinds of visible peaks by successive HTTL, and the most degree of MO(18) intramolecular charge transfer among all of the aggregation states. While the MO(18) hydrocarbon chain takes the all-trans conformation before HTTL, its conformation and orientation are most disarranged after HTTL for 2 min. Subsequently, the original conformation and orientation are recovered by degrees with successive HTTL, except after final HTTL for 18 min, when the orientation is again changed. On the other hand, the C(20)-d hydrocarbon chain maintains the all-trans conformation before and after HTTL. The orientation of the C(20)-d hydrocarbon chain after HTTL for 2 min is more ordered than that before HTTL, with the nature of the C(20)-d subcell packing changing from hexagonal to orthorhombic. During successive HTTL from 2 to 18 min, the C(20)-d orientation is gradually disorganized but with the orthorhombic nature remaining constant. Thus, the variations in the conformation and orientation of the MS(18) hydrocarbon chain and in the orientation of the C(20)-d hydrocarbon chain tend to change from ordered and disordered structures and turn to more disordered and ordered ones, respectively, where the former is mainly caused by the priority action of thermal energy and the latter by hydrophobic effect due to the presence of warm water. Consequently, it is suggested that there is a correlation between the degree of structural order for both hydrocarbon chains and the preferential action that takes place during HTTL.