This study aimed to compare the variability of the uterus during the menses phase (MP), follicular phase (FP), and luteal phase (LP) of the menstrual cycle using intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI).This prospective study was conducted at the Guangdong Provincial Hospital of Traditional Chinese Medicine between January 2022 and January 2023. Women of childbearing age (18-45 years) with appropriate progesterone levels were included in this study. Conventional magnetic resonance imaging and IVIM-DWI scans were performed during the MP, FP, and LP. The differences in IVIM-DWI-derived parameters between these phases were then compared, and the overlap was quantitatively described.The apparent diffusion coefficient (ADC) and pure molecular diffusion coefficient (D) values from the endometrium, uterine junctional zone (UJZ), and myometrium indicated statistical differences between the MP and FP and the MP and LP (ADC: endometrium, both P < 0.001; UJZ, P = 0.008 and P < 0.001, respectively; myometrium, P = 0.033 and P = 0.006, respectively; D: endometrium, both P < 0.001; UJZ, P = 0.008 and P = 0.006, respectively; myometrium, P = 0.041 and P = 0.045, respectively). The perfusion-related diffusion coefficient (D*) values from the myometrium indicated statistical differences between the FP and MP and the FP and LP (D*: myometrium, P = 0.049 and P = 0.009, respectively). The overlapping endometrium ratios between the MP and FP or LP were lower than 50% in the ADC and D values (ADC: overlapping of MP and FP: 33.33%, overlapping of MP and LP: 23.33%; D: overlapping of MP and FP: 40.00%, overlapping of MP and LP: 43.33%).The ADC and IVIM-derived parameters indicated differences in the uterus in diverse phases of the menstrual cycle, especially in the endometrium in relation to ADC and D values.