We investigate the molecular evolution and D/H abundance ratios that develop as star formation proceeds from dense cloud cores to protostellar cores. We solve a gas-grain reaction network, which is extended to include multi-deuterated species, using a 1-D radiative hydrodynamic model with infalling fluid parcels to derive molecular distribution in assorted evolutionary stages. We find that the abundances of large organic species in the central region increase with time. The duration of the warm-up phase, in which large organic species are efficiently formed, is longer in infalling fluid parcels at later stages. Formation of unsaturated carbon chains in the CH4 sublimation zone (warm carbon chain chemistry) is more effective in later stage. The carbon ion, which reacts with CH4 to form carbon chains, increases in abundance as the envelope density decreases. The large organic molecules and carbon chains are both heavily deuterated, mainly because their mother molecules have high D/H ratios, which are set in the cold phase. The observed CH2DOH/CH3OH ratio towards protostars is reproduced if we assume that the grain-surface exchange and abstraction reactions of CH3OH + D occurs efficiently. In our 1-D collapse model, the fluid parcels directly fall into the protostar, and the warm-up phase in the fluid parcels is rather short. But, in reality, a circumstellar disk is formed, and fluid parcels will stay there for a longer timescale than a free-fall time. We investigate the molecular evolution in such a disk by assuming that a fluid parcel stays at a constant temperature (i.e. a fixed disk radius) after the infall. The species CH3OCH3 and HCOOCH3 become more abundant in the disk than in the envelope. Both have high D/H abundance ratios as well.