In order to study effects of organic pollutants in irrigation water on soil physical properties, tracts of farmland in the Jiaokou Irrigation Zone, Shaanxi, that had long been irrigated with water polluted with organic contaminants were selected as subject in the study and some other tracts of farmland that had long been irrigated with unpolluted groundwater were set as control. They were both the same in soil condition and under the same climate condition and the same cultivation system. Composition of soil aggregates and microaggregates were measured by dry sieving and wet sieving, separately for analysis of variation of, dominant fractions of aggregates. Results show that long-term irrigation with organic-polluted water significantly decreased the contents of macro–aggregates (>10 mm) and micro-aggregates (<0.25 mm), but increased the content of “(quality) dominant aggregates” (1~5 mm). Correlation analysis shows that the content of water-stable aggregates was positively related with the content of soil organic matter, but insignificantly related to the mechanical composition of water-stable aggregates. Long-term irrigation with organic-polluted water also improved soil aggregate stability and enhanced soil aggregation, but reduced aggregate dispersion coefficient, an indication that soil structure was effectively improved. The findings prove that organic pollutants in irrigation water significantly improves soil structure and properties.