Decisions regarding the harvest time of rice are of critical significance to labor management and agricultural machinery dispatching to avoid unnecessary losses. However, the comprehensive composition of harvest loss and its variation rules remain poorly understood. Our objectives were to optimize the harvesting date to improve the paddy rice yield (PRY) of long and short-grain rice (LG and SUI) by minimizing the grain dry matter loss (GDML) and four kinds of mechanical losses (ML), i.e., header loss (HL), cleaning loss (CL), entrainment loss (EL), as well as un-threshed loss (UTL). For this aim, field experiments were performed (2017–2020) to assess the GDML, HL, CL, EL and UTL of the respective cultivar from 45 to 59 days after heading (45 DAH-59 DAH, i.e., 15 days) in Northeast China. Rice harvested at the initial stage of maturity exhibited maximal GDML, whereas, the GDML of the two cultivars declined first and then rose with the prolonged harvest date. For the ML, the HL and CL increased, while the EL and the UTL decreased for both cultivars from 45 DAH to 59 DAH. By examining the correlation between straw moisture content (SMC) and ML, significant correlations between SMC and four kinds of ML were demonstrated, which revealed the main factor of the variations of HL, CL, EL, and UTL during the whole harvesting period. The GDML showed no significant difference between LG and SUI, whereas the ML were significantly different. Moreover, as indicated from the difference in the proportion of harvest loss showed that the GDML was the critical factor determining the total loss for two cultivars throughout the harvest season. Overall, the results demonstrated that the optimal harvest date for LG was from 52 DAH to 53 DAH, and from 53 DAH to 54 DAH for SUI. Harvesting on a suitable date was a more effective way to enhance paddy rice yield than machinery operation adjustment, which ensured both quality and quantity of the rice. Once the harvesting was advanced or delayed, the operating parameters of the machinery should be adjusted to reduce the ML.