Aerobic composting is considered as an economically as well as environmentally friendly technology that prevents the diffusion of ARGs and ARBs from manure to farmland soil, on which many studies have been conducted. However, the transmission route and potential ecological risks of ARGs in soil-vegetable systems after application of manure at different maturity stages remain unclear. Therefore, through a pot experiment, this study analyzed the effects of manure composted from livestock excrement on ARGs and microbial community in different soil-vegetable systems, taking leafy plants (Shanghai green) and tuber plants (carrot) as examples. It was noted that the highly matured manure could reduce the ARGs contamination in soil and crops, and the ARGs in soil tended to accumulate in the direction of plant roots. The edible part of crops often had a more serious ecological risk of ARGs, and the potential pathogenic bacteria and ARGs could harm human health through exposure and dietary routes. In summary, this study provides new evidence for the transmission of ARGs in soil-vegetable systems with different mature stages of manure and highlights the potential safety risks of the transfer of antibiotic resistance from manure to soil and ultimately to the human food chain.