A series of 24 novel fluoroquinolone-uracil hybrids via various lengths linkers were designed, synthesized and evaluated for their antibacterial activities against both Gram-negative and Gram-positive bacteria, including resistant strains. All target compounds were fully characterized by 1H NMR, 13C NMR and high-resolution mass spectrometry (HRMS). Most of the tested FQs-AU hybrids displayed a significant antipathogenic activity. For instance, A3, A4, A5, A9, A10, A11, B16, C19 and C22 demonstrated broad-spectrum antibacterial activity against the 6 laboratory strains and 9 clinically isolated resistant strains, comparable to that of the reference antibiotic ciprofloxacin. Especially, the A4 displayed enhanced activity against MDR MRSE 62 (0.125 μg/mL) compared to ciprofloxacin (1 μg/mL), potent antibiofilm activity (8 μg/mL), and excellent systemic safety in vitro (CC50 > 128 μg/mL and HC50 > 200 μg/mL) and in vivo (100 mg/mL). Additionally, in vivo results demonstrated that A4 effectively cleared MRSE 62 and promoted infected wound repair in a mouse model. The above findings highlight FQs-AU hybrids as a potential pharmacophore for the development of novel and more efficient antipathogenic agents.