Micro-proppants with stronger portability have more potential to migrate to the massive micro-sized secondary fractures (SFs) or natural fractures activated by supercritical CO2 (Sc-CO2) fracturing in shale gas reservoirs. However, the transportation behaviour of micro-proppants in massive SFs has been scarcely studied to date. In this study, we report the simulation of micro-proppant migration across a fracture intersection during Sc-CO2 fracturing based on a combination of computational fluid dynamics and the discrete element method. A straight fracture intersection model was first validated against experimental data from an earlier study. Next, the influential factors, including fluid viscosity, cross angle, proppant diameter, fluid velocity and the ratio of proppant diameter to SF, were examined in the transportation behaviour of micro-proppants in Sc-CO2 fracturing. The results show that the poor proppant distribution in SFs is dominated by the ultralow viscosity of Sc-CO2, but the decrease of proppant diameter to 25 μm presents slurry flow behaviour, resulting in a migration distance around 8 times longer than that of 200 μm and much stronger proppant-carrying capacity into SFs. The transportation behaviour of micro-proppants into SFs depends on the suspended proppants concentration and the rolling proppants from the proppant embankment in the primary fracture (PF), determined by the combined effects of different factors. Fast fluid velocity of 0.2 m/s increases the priority of the proppant embankment formation in SFs. Cross angles greater than 45° limit the suspended proppants in SF, and the proppant embankment in the SF dominantly depends on rolling proppants from PF. Greater SF aperture facilitates proppants transportation into the SF due to the reduced bridging effect, but not into the PF. The key findings are optimized proppant-carrying capacity into SFs and improved stimulated volume during Sc-CO2 fracturing in shale reservoirs.