Low permeability saline aquifers, which are widely distributed around this world, have great potential for injected CO2 storage. Fluid flow in low permeability layers shows characteristics of low-velocity non-Darcy flow. A mathematical model considering the effect of threshold pressure gradient (TPG) for CO2 flow and storage in low permeability saline aquifer has been developed, and the corresponding numerical model has been formulated and solved. From the numerical results, we can conclude that the injection rate, cumulative CO2 injected, and the storage efficiency for the case with TPG are always less than those of the case without TPG because of the sharp pressure decline and increased energy consumption. Under this paper's calculation condition, the storage efficiency when considering TPG is about 10% less than the case without considering TPG. If the TPG effect was to be ignored in the design of CO2 storage in low permeability saline aquifers, the CO2 storage efficiency will be overestimated. The research enlarges the theoretical basis of carbon capture and storage (CCS) and provides a more accurate method to evaluate CO2 storage efficiency.