The conventional near-infrared laser transmission welding (LTW) process for joining dissimilar transparent polymers is limited by the need to incorporate optical absorbents, which compromises joint performance and raises biocompatibility concerns. To address these issues, this study proposed a surface modification technique using femtosecond laser ablation prior to the welding process. Experiments involved 520 nm femtosecond laser ablation of transparent polymers, followed by LTW of dissimilar transparent polymers using an 808 nm laser, with subsequent characterization and mechanical property evaluations. A maximum joint strength of 13.65 MPa was achieved. A comprehensive investigation was conducted into the physical and chemical mechanisms through which laser ablation improved the welding performance of dissimilar transparent polymers. The results demonstrated that laser ablation generated microstructures that serve as substitutes for optical absorbents while also facilitating the formation of numerous oxygen-containing functional groups. These enhancements improve miscibility and bonding performance between dissimilar polymers, enabling absorbent-free welding between ablated polycarbonate (PC) and polystyrene (PS). This work confirms both the feasibility and potential application of this process for direct LTW of dissimilar transparent polymers.