Middle Pleistocene–Holocene sediment sequences were obtained during International Ocean Discovery Program Expedition 385 in the Guaymas Basin. However, the age model is not well constrained due to a lack of stratigraphic datums and suitable dating approaches for this time interval. In this study, we analyzed the sedimentary carbonate content (wt% CaCO3) from Site U1546 as a proxy for biogenic carbonate production and compared it with the LR04 global benthic δ18O stack. The identification of 12 marine isotope stages from 21 correlation tie points establishes a refined chronology for the middle Pleistocene–Holocene sequence in the Guaymas Basin, and enables us to date the upper 354 m sediments back to ∼450 thousand years (kyr). Our data showed a broad range of wt% CaCO3 values, from ∼0 % to 64.1 %, with an average of ∼16.7 %. The relatively low carbonate contents are primarily attributed to the dominance of siliceous diatoms over calcifying coccolithophores under eutrophic conditions, and organic matter remineralization further reduces carbonate preservation. Additionally, our research underscores higher wt% CaCO3, linear sedimentation rates, and carbonate accumulation rates during interglacials compared to glacial periods, likely due to the preference of carbonate-producing coccolithophores for warmer temperatures. This suggests that climate change may have been the driver of the variation pattern of sedimentary carbonate content in the Guaymas Basin over the past ∼450 kyr. This study not only provides a refined chronology at multi-millennial time scale but also contributes critical data for cross-Pacific correlation with the Asian continental margins, enhancing the understanding of interactions between various climatic and oceanic processes on both regional and global scales.