Ostwald ripening behaviors of bubbles in porous medium are observed commonly in various fields, including CO₂ geological storage, preparation of porous materials, and fuel cells. A three-dimensional pore network model based on concentration coupling calculation has been developed to investigate the ripening characteristics of bubbles in porous medium on a pore scale. This model takes into account the shape of bubble, the structure of porous medium, and mass transfer between gas and liquid. By solving the gas phase concentration of each pore body in the three-dimensional pore network, the model can track the evolution process of each bubble. A microfluidic chip with a four-pore structure is used to validate the reliability of the model through visual experiments. To analyze the effect of porous medium heterogeneity on the bubble ripening process, two different three-dimensional pore network structures with varying pore sizes are constructed and the ripening processes of bubbles in two regions are simulated numerically. The results show that the initial distribution of bubbles can affect the ripening process of porous medium. When bubbles are uniformly distributed, in the ripening process, they exhibit regular and systematic changes in their spacing. However, in the case of uneven bubble distribution, as the bubbles transfer from smaller pore region to larger pore region, they also undergo individual mass transfer towards the larger bubble region in their respective areas. Consequently, the remaining bubbles no longer maintain a spaced distribution pattern. Additionally, the differences in initial size among bubbles can accelerate the ripening process, resulting in a significantly shorter ripening time than that in a uniform distribution. The choice of pore number has a significant influence on continuous-scale equivalent parameters, such as average capillary pressure and saturation. As the number of pores increases, the capillary pressure and saturation exhibit a more regular, nonlinear variation. A relationship between capillary pressure and saturation in the small pore region and in the large pore region are established, which deviate from the assumptions made in the existing literature. This result provides important guidance for constructing the continuous-scale ripening model that can be used to predict the evolution process of CO₂ during geological storage and provide guidance for studying the influence mechanism of heterogeneity during long-term CO₂ storage.