Abstract. Efficient and accurate simulating fluid flow and heat transport underground plays an important role in groundwater migration and geothermal resource prediction, etc. Rock fractures are complex in geological settings, they exhibit multiple scale properties and the fracture pattern is varied for different geological conditions. Modeling and upscaling permeability for fractured porous rocks are both important and sophisticated approaches in the numerical simulation. Nevertheless, there is often a lack of efficient and flexible methods to connect these two processes. In this study, a novel methodology combining modeling and upscaling permeability for fractured porous rocks in proposed and an open-source software, UpsFrac, is developed to consider complex fracture geometries in discrete fracture models (DFM) that are created determinedly and stochastically. The software can characterize complexity of fractured porous rocks such as power law (fractal) length distribution, correlations between fracture length and aperture, and the effect of rock matrix properties. The state-of-the-art upscaling method, the multiple boundary method (MFU), is applied to calculate equivalent fracture permeability, which links the fine-scale discrete fracture model to the coarse-scale equivalent fracture model. The code is in Matlab and is based on fracture modelling code ADFNE and reservoir simulation code MRST, which can easily run DFM ensembles for uncertainty analysis. The code is available in open repositories to encourage modeling and upscaling of complex fractured porous rocks, allowing users to develop their own routines within the current framework and to benefit a broader community.