The exploitation of low permeability carbonate oil reservoirs is significantly challenged by the widespread use of horizontal well groups and the injection of large volumes of low temperature fluids into high temperature reservoirs. These practices introduce two primary issues: the deviation from Darcy flow due to the low permeability, leading to pre-Darcy flow, and the substantial impact of temperature fluctuations on pre-Darcy flow behavior, triggered by the injection of cooler fluids. Existing flow models have not adequately addressed the temperatures’ influence on pre-Darcy flow, and there is a paucity of the related numerical simulation studies. To address these issues, a temperature-dependent pre-Darcy (TDPD) flow model is proposed which integrates the temperatures’ effects on both the boundary layer thickness and the fluid yield stress, deriving from capillary flow model and boundary layer theory. A corresponding thermal-hydraulic numerical simulation method is also established, which accounts for the TDPD flow to assess its impact on the production performance of horizontal wells. The comparisons with Darcy model demonstrate that TDPD model is able to capture the temperature-induced variations in pre-Darcy flow behavior, offering a more plausible and rational approach. Simulations of water flooding in horizontal well group considering TDPD flow predict lower cumulative oil production and average reservoir pressure compared to Darcy flow. The proposed TDPD model, along with the findings and insights presented in this study, is poised to make a substantial contribution to the evolution of percolation theory and the simulation of carbonate oil reservoirs.