To study the distribution characteristics of typical pollutants in soil aggregates using different sieving methods, urban and arable soils were collected from Beijing and separated to different sizes by dry and wet sieving methods, to analyze present concentrations of inorganic chlorine and nine typical heavy metals (Cr, Mn, Co, Ni, Cu, Zn, Cd, As, and Pb). Results revealed that the distribution of wet-sieved aggregates was biased towards microaggregates (<250 μm), while the contrary result was found for the dry sieving method. Inorganic chlorine was more likely to be enriched in <53 μm fractions attained by both sieving methods. However, the content of inorganic chlorine in wet-sieved aggregates was significantly lower than in those that were dry sieved, which means the water’s effect on soluble ions was more pronounced. Heavy metals in urban soils were preferentially enriched in microaggregates no matter what kind of sieving method was applied. As for Mn and As found in agricultural soils using the dry sieving method, they were preferentially enriched in the fractions of 1000−2000 μm and 250−1000 μm, while the other seven heavy metals were preferentially enriched in <53 μm fractions, indicating that Mn and As in agricultural soils were easily transferred in aggregates with different particle sizes. Samples with particle sizes <53 μm showed the highest distribution factors for all heavy metals when the wet sieving method was applied. The dry sieving method resulted in a higher mass loading of heavy metals in coarser fractions and lower proportions in finer fractions. Results of a potential ecological risk analysis showed that the ecological risk (Eri) value of Cd found in aggregates by the different sieving methods was significantly different (p < 0.05). The findings suggest that different sieving methods could result in different occurrence patterns of pollutants in the soil aggregates of different land use types.