The modified multiple platform method (MMPM) is a classical sleep deprivation model. It has been widely used in behavioral and brain research, due to its effects on physical and mental functions. However, different MMPM protocols can promote distinct effects in rats. Although the MMPM has been proved to induce central fatigue, the effects of different durations of subjection to the MMPM remain undetermined. This study aims to investigate the changes in behavior, N-Methyl-d-Aspartate receptor 1 (NR1) and 2A (NR2A), as well as the ultrastructural alteration in the hippocampus after different MMPM modelling, to compare the central fatigue effect induced by dynamic MMPM. Rats were randomly divided into four groups: 5-, 14- and 21- day MMPM groups, and a control group. Each MMPM group underwent a 14-hour daily MMPM modelling. After each training session, open field and elevated plus maze tests were performed. Corticosterone levels were detected by ELISA, and the hippocampal NR1 and NR2A were measured by RT-PCR and Western blot analysis. In addition, ultrastructural changes in the hippocampal cornu ammonis 1(CA1) region were determined by transmission electron microscopy (TEM). The findings showed that the 5 and 14 days of MMPM induced a high-stress state, while the 21 days of MMPM induced anxiety and degenerative alteration in the hippocampal morphology. Additionally, hippocampal NR1 and NR2A gene expression decreased in all MMPM groups, whereas the protein expression only decreased in the 21-day group. Overall, different durations of MMPM caused distinct behavioral and brain changes, and the 21 days of MMPM could induce central fatigue.