To evaluate the effects of straw and lime application on soil micronutrients and tomato yield, soils from plots amended with no fertilizer (CK), chicken manure (M), chicken manure + straw (MR), chicken manure + lime (MCa), chicken manure + straw + lime (MRCa) were collected. The results showed that:(1) Straw increased the contents of DTPA-extractable Fe, Mn and Zn in soil, MR caused 3.2%, 80.9% and 15.1% increase compared with M, respectively. Lime increased the contents of DTPA-extractable Fe, Mn, Cu, Zn in soil. The DTPA-extractable Fe, Mn, Cu and Zn contents in soil were significantly correlated with soil pH values and organic matter contents (P<0.01). (2) The micronutrients decreased as the aggregate sizes decreased. Adding straw and lime increased the DTPA-extractable Mn content in soil aggregate of 1~0.25 mm, MRCa caused 6.6%~46.6% increase compared with other treatments. Straw increased the DTPA-extractable Zn content in the aggregate<0.25 mm. The DTPA-extractable Fe content in soil was positively correlated with that in aggregate of <1 mm (P<0.01), the DTPA-extractable Mn and Zn contents were positively correlated with those in all aggregates sizes (P<0.01), and the DTPA-extractable Cu content in soil was positively correlated with that in aggregate of 1~0.25 mm (P<0.01). (3) Straw or lime increased tomato yield, the MRCa treatment had the highest yield, which was 12.6%~151.1% higher than other treatments. The DTPA-extractable Fe and Cu contents in soil were positively correlated with yield. The DTPA-extractable Fe had a direct effect and it sdecision coefficient was the highest. The DTPA-extractable Cu had an indirect effect. Therefore, straw and lime could alleviate the shortage of micronutrients in greenhouse soil, and the maximum crop yield could be obtained, which guaranted the sustainable utilization of soil in greenhouse and the sustainable development of greenhouse agriculture.