Water-rock reactions within the reservoir during karst-based geothermal exploitation can lead to variation of porosity and permeability, affecting the system's thermal performance. A multi-field coupled thermal-hydraulic-chemical model considering the pore changes was developed to investigate the mechanism of water-rock reaction on the evolution of pores and permeability during the production process of karst-based geothermal reservoirs. The mechanism of water-rock reaction on reservoir pore-permeability evolution under thermal-hydraulic-chemical coupling is revealed, and the evolutionary characteristics of pore-permeability parameters and their evolutionary impact on the system heat extraction performance are investigated. The results show that under undersaturated injection conditions, the concentration and porosity distribution present a ring shape, which is caused by dissolution reactions occurring in the injection wells and swept front regions, and precipitation reactions occurring in the intermediate regions. After 30 years of production, the porosity and permeability at the injection wells increased by 19.3% and 73.6%, respectively, and the porosity and permeability at the production wells decreased by 0.11% and 0.32%, respectively. The injection-production differential pressure of the case considering pore deformation was 21.7% lower than that of the case without considering pore deformation. This study is instructive for the accurate prediction of carbonate karst-based reservoir production and development program optimization.