In order to determine the effect of organic fertilizer application on the calcium distribution and aggregate in cultivated brown soil, the field cultivated brown soil fertilized for nearly 30 years was taken as study object. The soil aggregate was classified by dry sieve method, while the effect of single and combined application of organic fertilizer on the distribution of different calcium forms was analyzed. The results showed that the single application of organic fertilizer could increase ＞1 mm graded aggregate content compared with control, the increment increased with the amount of organic fertilizer and could reach 66.68%. Combined nitrogen and phosphorus fertilizer application reduced ＞1 mm graded aggregate content compared with the single application of organic fertilizer. The single application and combined nitrogen and phosphorus fertilizer application decreased 0.25～1 mm graded aggregate content compared with control, while the highest decrease was 15.20%. The single application and combined nitrogen and phosphorus fertilizer application increased total calcium content in soil. The calcium content of the single application of organic fertilizer was higher than that of combined nitrogen and phosphorus fertilizer application. The highest increment of calcium (11.67%) was the treatment received higher organic fertilizer application. The highest total calcium content was in the ＞1 mm graded aggregate of the treatment received single organic fertilizer, while the highest total calcium content was in the 0.053～0.25 mm graded aggregate of treatment received combined nitrogen and phosphorus fertilizer. The single organic fertilizer and combined nitrogen and phosphorus fertilizer application increased water-soluble calcium content in each graded aggregate. The single application of organic fertilizer improved exchangeable calcium content in soil, while the trend was reversed when combined nitrogen and phosphorus fertilizer was applied. The single application of organic fertilizer and combined nitrogen and phosphorus fertilizer all increased acid soluble calcium content in soil. Correlation analysis indicated that the total calcium content in each aggregate grade was the key factor effects the distribution of the various forms of calcitonin. Therefore, long-term organic fertilizer application not only increased the larger grade aggregate content in soil, but also enhanced the calcium content in larger aggregate.