Extensive karst fissures exist in areas of karst high geological background and soils formed by the development of carbonate rocks are rich in heavy metal(loid)s. However, there are insufficient studies related to soil heavy metal(loid)s in shallow fissures, and the risk is unknown. An accurate understanding of the distribution of heavy metal(loid)s in these soils and their influencing factors is essential to further reveal the transport patterns of heavy metal(loid)s in karst fissures. In this study, 15 natural shallow fissured soil profiles were selected from a high geochemical background area in southwest China. We examined the vertical distribution patterns of heavy metal(loid)s within the fissures and the factors controlling them. The results showed that the cadmium (Cd) exceedance rate was highest in shallow fissured soil profiles, exceeding the background value by 4 times, and the coefficient of variation for Cd was also the highest, averaging above 60%. Lead (Pb), zinc (Zn), and arsenic (As) followed. The Cd content was highest at a depth of 0-80 cm, at 3.07 mg/kg. The pollution index (PI) results indicate that Cd is highly polluted (PI > 3), while Pb, As, and Zn are moderately polluted (1 < PI <= 3). The geoaccumulation index (I-geo) results indicate that Cd is moderately polluted (1 < I-geo <= 2), Pb and Zn are unpolluted to moderately polluted (0 < I-geo <= 1), and As is unpolluted (I-geo < 0). The results showed that the Cd pollution was higher than the other 3 types. Furthermore, the pollution index increases with soil depth. The RAC method analysis results show that the potential risk of Cd in 0-20 cm (25.68%) is higher than that in 80-100 cm (19.20%). Soil moisture (SM), soil texture, and cation exchange capacity (CEC) emerged as the primary factors influencing the vertical distribution of Cd, As and Zn (p < 0.01). Clay content enhances heavy metal enrichment in soil, while sand and silt have the opposite effect. There is no strong correlation between Pb and the physical and chemical properties of soil, as Pb is mainly affected by human pollution. This indicates that the study area is not only affected by geological factors, but also by human activities that exacerbate heavy metal pollution. In conclusion, the vertical distribution of heavy metal(loid)s in shallow fissured soil profiles exhibits variability, influenced by a range of factors. These outcomes contribute to understanding the pattern of heavy metal distribution in shallow karst fissures and offer insights for managing soil heavy metal pollution in karst regions.