Abstract: Saline-alkali soil improvement with microbe is a green and sustainable method, and Congo red is an ideal indicator with low toxicity and sensitive colour-changing ability to pH value. To reduce the soil pH value rapidly and provide essential foundation for the survival of plants, the Congo red was added into the culture medium to screen the strain with both well salt tolerance and high yield of organic acid, and finally the strain named SQ21 was successfully isolated from coastal saline soil, and was identified as Aspergillus niger after analyzing its morphological characters and ITS-rDNA sequence. After applying SQ21 into saline-alkali soil, the results showed that the soil pH value reducing degree was positively related to the dosage of SQ21, and after applying 3.18×1010 cfu spores of SQ21 into 500 g saline-alkali soil, the soil pH value decreased by 2.24 after 50 days. After adding bran, compound fertilizer or sodium nitrate as base fertilizer into 500 g salinealkali soil, and applying 7.96×109 cfu spores of SQ21 into the soil every 2 weeks, the soil pH value of each treatments reduced by 1.12, 0.6 and 1.37 after 56 days. The comparison of the growth of chrysanthemum on saline-alkali soil under different treatments showed that the height and crown diameter of chrysanthemum treated with SQ21 and bran increased the most, and the comprehensive evaluation of the pH value reducing degree and the growth of chrysanthemum indicated that the combination of SQ21 with bran was better than SQ21 with compound fertilizer or sodium nitrate. The research proved that the SQ21 could reduce the pH value of saline-alkali soil and promote plant growth.