In this study, a series of 10,11-difluoromethylenedioxy-pyrrolo[3,4-b]quinoline alkaloid derivatives were designed as novel dual Topo I/DDX5 inhibitors, demonstrating excellent antitumor activity. Among them, compound A10 was identified, exhibiting potent antiproliferative activity across four human cancer cell lines and a favorable low-toxicity profile in vivo. It significantly inhibited colony formation and migration in colorectal cancer cells, induced DNA damage response pathways, suppressed the expression of antiapoptotic proteins, and stimulated ROS generation, leading to cell cycle arrest and apoptosis. Moreover, A10 exhibited superior transmembrane transport capacity and was not a substrate of the drug-resistant efflux pump protein P-gp, which enhanced antitumor efficacy and reduced the risk of drug resistance. In colorectal cancer HT-29 xenograft models, A10 demonstrated robust antitumor efficacy with a favorable safety profile. Metabolite profiling revealed that the introduction of difluoro substitution effectively reduced metabolic risk. Collectively, A10 represents a promising candidate for further preclinical development against colorectal cancer.