Based on the 180 soil samples collected from Luzhou’s tobacco planting area, the spatial variability characteristics of soil available microelement contents (available Fe, Mn, Cu, Zn, B and Mo) as well as their influencing fators for instance fertility factors and topgraphic factors with correlation for ecological suitability zone planning of tobacco and microelement fertilizer apply were analyzed using by geostatistics and GIS technology. The results showed that the average contents of soil available Fe, Mn, Cu, Zn, B and Mo were 70.42, 46.72, 2.33, 1.75, 0.34 and 0.17 mg/kg, respectively, showing the spatial distribution pattern with high contents in south and east regions while low contents in north and west regions on the whole. Semi-variance analysis revealed available B and Mo fit for the spherical model while the other elements for the exponential model. The ratios of nugget to sill were between 25% and 75%, indicating the spatial varibilities of the six soil available microelements were affected by both the structural and random factors. For fertility factors, soil available microelement contents had no significant correlation with total potassium, but positively correlated with soil organic matter, nitrogen, phosphorus and available potassium and negatively correlated with pH on the whole. For topgraphic fators, slope and aspect had no significant correlation with soil available microelement contents while altitude had significant or extremely significant correlations with available Mn, Cu and Mo. In comparison, soil fertility factors played a more important role on the spatial variabilities of soil available microelement contents in the study area.