The contents and eco-stoichiometric ratios of soil carbon, nitrogen, and phosphorus have important effects on crop nutrient supply. It is still unclear how long-term straw incorporation affects the carbon, nitrogen, and phosphorus contents and eco-stoichiometric ratio of soil aggregates in paddy fields. In this study, the double-cropping rice field was taken as the research object, and three treatments of only applying chemical fertilizer (CK), low amount straw incorporation + chemical fertilizer (LS), and high amount straw incorporation + chemical fertilizer (HS) were set up. Soil aggregate composition and its contents of carbon, nitrogen, and phosphorus were measured in 9~10 years after straw incorporation, and the distribution, average weight diameter, and eco-stoichiometric ratio of soil aggregates were also analyzed, so as to clarify the contribution of soil aggregates with different particle sizes to carbon, nitrogen, and phosphorus nutrients and the characteristics of the ecological stoichiometric ratios under long-term straw incorporation in double cropping rice fields. The results showed that in 9~10 years after straw incorporation, compared with CK, HS and LS treatment significantly increased the proportion of water-stable aggregates with the particle size of > 0.25 mm (R0.25) and mean weight diameter (MWD). HS treatment significantly increased the total carbon (TC) and total nitrogen (TN) contents of water-stable aggregates with the particle sizes of > 2 mm, 0.25~1 mm, 0.053~0.25 mm and < 0.053 mm, and the particle size with the largest increase of TC and TN was 0.25~1 mm, with an increase of 28.1% and 22.9% respectively, but had no significant impact on the total phosphorus (TP) content. Compared with CK, HS and LS treatments significantly increased the contribution rate of water-stable aggregates > 2 mm to soil TC, TN and TP, which was helpful to improve the nitrogen and phosphorus uptake of rice. Compared with the CK, HS treatment improved the nitrogen phosphorus ratio and carbon phosphorus ratio of water-stable aggregates (> 2 mm, 1~2 mm, 0.053~0.25 mm and < 0.053 mm), which was beneficial for improving nitrogen availability in rice fields and did not limit phosphorus supply with the carbon phosphorus ratio not exceeding the threshold. This study showed that the high amount of straw (6 t/hm2) incorporation at can improve the stability of water-stable aggregates, increase soil carbon and nitrogen storage, and the aggregate nitrogen phosphorus ratio, which has a good effect on improving soil structure and nitrogen supply in paddy fields.