Abstract: Microplastics (MPs) pollution in agricultural soils has emerged as a global environmental issue. MPs compromise soil health by altering soil physical structure, inhibiting microbial activity, and interfering with nutrient cycling, thereby affecting crop growth and reducing agricultural product quality. Given the dense population and high consumption of plastic products in South China, microplastic pollution in its agricultural land is of particular concern. This study collected 34 agricultural soil samples from six ‘Vegetable Basket’ base in a city in South China to systematically analyze the abundance and morphological composition of soil MPs. Source apportionment was conducted using the positive matrix factorization (PMF) model, and ecological risks were assessed by integrating four distinct evaluation methods: the potential ecological risk index (RI), polymer hazard index (PHI), pollution load index (PLI), and Nemerow pollution index (NPI). The results indicated that: (1) The abundance of MPs in the 34 agricultural soil samples from the six bases ranged from 344.27 to 7702.79 items/kg dry weight (dw), with the average level in vegetable bases (2026.06 items/kg dw) was higher than that in fruit bases (1327.28 items/kg dw). (2) The predominant shapes of MPs were fragments and fibers, with particles < 0.5 mm accounting for the highest proportion. The most prevalent colors were white and transparent, and the primary polymer compositions included polyethylene (PE) and polyethylene terephthalate (PET). (3) PMF analysis revealed that agricultural water, residual agricultural film, and discarded agricultural materials were the main sources of MPs in the soils. (4) Ecological risk assessment indicated that most bases exhibited relatively high ecological risks due to the presence of MPs with high toxicity, such as polyurethane (PU) and polyvinyl chloride (PVC). In conclusion, soil microplastic pollution is widespread and poses high ecological risks in the ‘Vegetable Basket’ base of a city in South China. Vegetable bases were more severely contaminated than fruit bases, highlighting the need for focused attention on the continuous input and degradation risks of highly toxic polymers such as polyurethane (PU) and polyvinyl chloride (PVC).