The stability of soil aggregates provide physical protection for soil carbon, while soil carbon promotes the formation of soil aggregates. To evaluate the effects of long-term straw and quicklime application on soil aggregates stability and total carbon (TC) accumulation at aggregate, soils from plots amended with M (chicken manure), MR (chicken manure + straw), MCa (chicken manure + quicklime), MRCa (chicken manure + straw + quicklime) were collected compared with CK (no-fertilizer). Soil was separated into five size fractions (5~2, 2~1, 1~0.5, 0.5~0.25, < 0.25 mm) by wet-sieving. The results showed as follows:(1) Straw return or liming increased the distribution of > 0.25 mm size fractions, MR and MCa caused 123% and 37% increase relative to the M, respectively; while application of straw and quicklime together had a significant effect on the distribution of 5~2 mm size fraction, compared with MR, MCa and M, the MRCa caused 12%, 59% and 141% increase, respectively. (2) Application of straw and quicklime could increase the MWD, GMD and R_0.25. MR treatment had the highest MWD, GMD and R_0.25, followed by the MRCa treatment, MR and MRCa were significantly higher than those of MCa, M and CK. (3) Addition of straw and quicklime could increase the TC content, compared with MR, MCa and M, MRCa caused 20%, 40% and 55% increase, respectively; straw return and liming significantly increased the TC content of 5~2 mm size fraction; liming could increase the TC content of 0.5~0.25 mm size fraction; both straw and lime could significantly increase the contribution of TC in the >0.25 mm size fractions to the bulk soil TC. (4) TC content was positively correlated with the distribution of 5~2, 2~1, 1~0.5 mm size fractions, and negatively correlated with the distribution of < 0.25 mm size fraction. MWD, GMD and R_0.25 were positively correlated with the distribution of > 0.25 mm size fractions, and negatively correlated with the distribution of < 0.25 mm size fraction. Therefore, straw return and liming could improve the soil structure and carbon level. These findings were beneficial to alleviate the problem of soil structural fission caused by long-term continuous cropping in the agricultural production of greenhouse.