Gravity-driven membrane (GDM) filtration technology has been extensively in the employed drinking water treatment, however, the effect filtration mode (i.e., dead-end mode vs. cross-flow mode) on its long-term performance has not been systematically investigated. In this study, pilot-scale GDM systems were operated using two submerged filtration mode (SGDM) and cross-flow mode (CGDM) at the gravity-driven pressures 120 mbar and 200 mbar, respectively. The results showed that flux stabilization was observed both in the SGDM and CGDM during long-term filtration, and importantly the stabilized flux level of CGDM was elevated by 3.5–67.5%, which indicated that the filtration mode would not influence the occurrence of flux stability, but significantly improve the stable flux level. Interestingly, the stable flux level was not significantly improved with the increase of driven pressure, and the optimized driven pressure was 120 mbar. In addition, the GDM process conferred effective removals of turbidity, UV254, CODMn, and DOC, with average removals of 99%, 43%, 41%, and 20%, respectively. With the assistance of cross flow to avert the overaccumulation of contaminants on the membrane surface, CGDM process exhibited even higher removal efficiency than SGDM process. Furthermore, it can be found that the CGDM system can effectively remove the fluorescent protein-like substances, and the intensities of tryptophans substance and soluble microbial products were reduced by 64.61% and 55.08%, respectively, higher than that of the SGDM. Therefore, it can be determined that the filtration mode played an important role in the flux stabilization of GDM system during long-term filtration, and the cross-flow filtration mode can simultaneously improve the stabilized flux level and removal performance.