We investigated the associations of time-dependent DWI, non-Gaussian DWI and CEST parameters with histological biomarkers in a breast cancer xenograft model. 22 xenograft mice (7 MCF-7 and 15 MDA-MB-231) were scanned at 2 diffusion times (Td= 2.5/ 5 ms) with 11 b values (0–600 s/mm2), and 9/ 27.6 ms with 17 b values (0–3000 s/mm2). The apparent diffusion coefficient, ADC0 − 600, shifted ADC, sADC200 − 1500 and the ADC change with Td, as well as IVIM and non-Gaussian diffusion parameters were estimated. CEST images were acquired and the amide proton transfer signal intensity (APT SI) were measured. The sADC200 − 1500 change and combined ADC change (ADC0 − 600, 2.5 ms with sADC200 − 1500, 27.6 ms) was significantly larger for MCF-7 group, and the combined ADC change was positively correlated with Ki67max and APT SI. ADC0 decreased significantly in MDA-MB-231 group and K increased significantly with Td in MCF-7 group. APT SI and cellular area had a moderately strong positive correlation in MDA-MB-231 and MCF-7 tumors combined, and there was a positive correlation in MDA-MB-231 tumors. There was a significant negative correlation between APT SI and the Ki-67-positive ratio in MDA-MB-231 tumors and when combined with MCF-7 tumors. The associations of combined ADC change and API SI with Ki-67 parameters indicate that the Td-dependent DW and CEST parameters are useful to predict the histological markers of breast cancers.