Soil chemical and topographic properties are two important factors influencing available micronutrient distribution of soil in the horizontal dimension. The objective of this study was to explore the relative influence of soil chemistry (including soil pH, soil organic matter, total nitrogen, available phosphorus, and available potassium) and topography (including elevation, slope, aspect, and wetness index) on the availability of micronutrients (Fe, Mn, Cu, Zn, and B) using structural equation modeling (SEM) at the watershed scale. To do this, levels of soil micronutrients, pH, soil organic matter, total nitrogen, available phosphorus, available potassium, and topographic factors were measured at 523 sampling points of Fanshi County on the Chinese Loess Plateau, and the spatial distribution of soil available micronutrients were analyzed by geostatistical method. The results showed that topography had both direct effects and indirect effect on some soil micronutrients, while the indirect effect indicated effects from topography on soil chemistry and then further on micronutrient concentration. Soil chemistry had direct effects on levels of all soil micronutrients, and topography had direct effects on levels of all micronutrients except for Cu and B, and indirect effects on Fe, Zn, and B. The direct effect of soil chemistry on Fe levels was greater than the total effects (including both direct and indirect) of topography. Topography had a stronger direct effect on Mn than soil chemistry, and topography had less direct but stronger total effects on Zn than soil chemistry. Soil chemistry directly influenced both Cu and B, but topography only influenced B in an indirect manner. The semivariance indicated that the micronutrients had moderate spatial dependency except for B which had weak spatial dependency. Within the spatial distribution of the micronutrients, there was a zone in the middle of the watershed with lower values than in the northern and southern areas for Fe, Mn, Zn, and B, which were related to the characteristics of topography and soil chemistry. These results may guide the management of soil micronutrients of the Chinese Loess Plateau and other similar regions in the world.