Abrasive Water Jet (AWJ) technology is widely used in mining. To explore how rock heterogeneity and natural cracks affect rock fragmentation, a numerical model using the pixel method was developed for jet-induced rock breakage. This method effectively represents rock cracks and improves computational efficiency. The study found that AWJ causes more damage in rocks with natural cracks compared to Pure Water Jet (PWJ), with significant differences in damage extent. Under PWJ, intact rocks showed minimal fracturing, while rocks with natural cracks experienced increased crack depth, length, and number. However, under AWJ, the overall fracture levels were similar in both rock types. Notably, rocks with natural crack had longer cracks under AWJ, setting the stage for more extensive fragmentation. These results offer theoretical support for using water jets in mining extraction. Display omitted •Utilizing a pixel-based modeling approach enhances computational efficiency.•The fracturing effects on intact and naturally cracked rocks were compared.•The effect of natural cracks on the macroscopic crushing patterns of rocks was investigated.