Aims Little research has been done on natural environmental factors that impact phenotypic characters of Arabidopsis thaliana populations in their natural habitat. Our objective was to determine the distribution patterns of phenotypic characters and the relationship of phenotypic characters and environmental factors of A. thaliana populations. Methods From May to June 2009, we studied ten populations in the northern Tianshan Mountains. We placed 10 m × 10 m quadrats at each population plot, each comprised of about 400 smaller (0.5 m × 0.5 m) quadrats, and investigated the distributional patterns of populations and nine environmental factors. Twenty A. thaliana plants were selected, and ten phenotypic characteristics (branch number, plant height, plant biomass, root biomass, single fruit weight, fruit number per plant, fruits weight per plant, fruit length, fruit dehiscence force, fruit weight per plant/total weight) were measured. Variance, principal component and regression analyses were used. Important findings All phenotypic characteristics except branch number showed significant differences among populations, which indicated that there is strongly plasticity in the nine characters. The results of the analysis of variance and coefficients of variance indicated that fruit length and fruit dehiscence force have little variation within and among populations. Phenotypic characters varied little among different mountains, altitudes, latitudes and longitudes. The results indicated that A. thaliana populations mainly distributed on sandy soils that contained lower HCO3–, pH values and higher soil organic carbon (SOC). The distribution frequencies of A. thaliana within populations are very low, ranging from 1.56% to 10.69%, with spatial autocorrelation distances being 15.4 to 46.7 cm and variable. Ten populations were all highly clumped in their distribution (p < 0.01), which was significantly correlated with the fruit dehiscence force, while the fruit dehiscence force increased as environmental stress increased. Results suggested that the growth and distribution of A. thaliana in the northern Tianshan Mountains are influenced mainly by microenvironments. In dry environments, A. thaliana would increases the ratio of reproduction distribution and produce poorly dehiscent fruits that make seeds disperse around maternal plants and utilize feasible habitats.