Holographic lithography has garnered significant research attention in the production of 3-D micro/nano structures due to its high efficiency. To delve deeper into the morphological changes within these 3-D structures and evaluate the impact of exposure system design on production, a comprehensive exposure dose model within the photoresist was developed, rooted in holographic lithography principles. Additionally, a morphology evolution model for 3-D micro-nano structures was formulated. By utilizing these established models, theoretical analysis was conducted to investigated key variables influencing the contrast of the exposure field, including light source polarization, exposure substrate reflection, and incident light phase drift. Simulation results indicate that, within the classical reflective holographic lithography system, the transverse electric and transverse electric(TE-TE) polarized incident light exhibits superior contrast (above 0.95) across various incident angles, surpassing other polarization combinations significantly. Moreover, the reflectivity of the exposure substrate significantly influences contrast in the substrate’s normal direction, showing a positive correlation. Importantly, significant and low-frequency drifts in the incident light’s relative phase result in a notable decrease in exposure field contrast. Thus, actively mitigating environmental and internal disturbances is crucial for maintaining a high-contrast exposure field. This study provides a reference for the parameter optimization design of reflective holographic lithography systems.