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Trace elements in farmland soil are important indicators of soil quality and farmland health, and also maintain the nutrient balance and promote the healthy growth of plants. In this study, taking Conghua District of Guangzhou city as the study area, the effects of topography, soil, land use, and other factors on trace elements in soil were investigated, and the spatial variability of boron (B), manganese (Mn), molybdenum (Mo), copper (Cu), and zinc (Zn) in farmland soil in a typical red soil region were mapped using a geographically weighted regression (GWR) method. The pH and land economic index (LEI) were important factors affecting the changes in trace element concentrations in the five soils, and the Cu and Zn concentrations were clearly affected by human factors. In the study area, 86.99% of B measurements were classified as low and very low levels, 50.61% and 49.20% of Mo measurements were also low and very low, 71.79% of Mn measurements were classified as moderate, while 91.02% of Cu and 52.95% of Zn measurements were classified as high. After a cross validation, the GWR Kriging (GWRK) model results of each element were relatively stable, and the order of the fitting coefficient (R2) was Cu > Zn > B> Mn > Mo. This study clarifies the spatial distribution and influencing factors of soil microelements in the studied region. This information can be used to improve the nutrient imbalance, further guide agricultural production, strengthen the management of farmland, and improve the healthy productivity of cultivated land. [ABSTRACT FROM AUTHOR]