The paper aims to investigate the effects of compound application of organic fertilizers with microbial fertilizers on photosynthetic characteristics, antioxidant capacity and yield and quality of organic Lycium barbarum in saline and alkaline land in Ningxia region. In 2023, a fertilizer experiment was carried out at the wolfberry base of Liu Chuanjing Organic Wolfberry Professional Cooperative in Zhenbeibao Unity Village, Yinchuan City, Ningxia. Four fertilizer treatments were set up, namely, single application of organic fertilizers (MD), organic fertilizers and balanced light and photosynthetic fungal fertilizers compost rotting furrow application (MPG), single application of balanced, photosynthetic fungal fertilizers (MP), and no application of any fertilizers (absolute control, CK), and the results were obtained by analyzing the interrelationships between the leaf physiological characteristics and yield quality of wolfberry. The results showed that: the application of microbial fungal fertilizer could significantly improve the photosynthetic parameters of L. barbarum, increase the antioxidant capacity, and inhibit the accumulation of lipid membrane peroxidation products, thus significantly improving its yield and quality, and the overall performance of MPG treatment was the best. Compared with CK, the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr) and SPAD were increased by 47.83%-122.09%, 32.26%-69.31%, 36.74%-96.94%, and 3.65%-25.52%, respectively, with MD, MPG, and MP treatments; meanwhile, superoxide dismutase (SOD), peroxidase (POD) and catalase activity (CAT) increased by 3.22%-12.30%, 8.59%-28.53% and 2.76%-32.76%, respectively; whereas flavonoids content, Lycium barbarum polysaccharide content, betaine content and total dry fruit yield increased by 7.07%-40.46%, 18.70%-28.43%, 1.22%-35.37% and 23.80%-55.43%. Correlation analysis showed that the L. barbarum yield was positively correlated with Pn, Ci, Tr and SPAD in a highly significant way; flavonoids content, polysaccharide content and betaine content were positively correlated with physiological characteristics such as Pn, Ci, Tr, SPAD, SOD, POD and CAT in a significant or highly significant way; while the quality and yield indicators were negatively correlated with MDA in a significant or highly significant way. The principal component analysis showed that the composite score of each treatment was MPG>MP>MD>CK. Therefore, the compound application of organic fertilizers with microbial fertilizers could consistently improve the SPAD value, Pn, Gs and Tr of L. barbarum leaves; optimize the antioxidant capacity of L. barbarum leaves and inhibit the accumulation of MDA; and then promote the growth of the plant and significantly increase the content of flavonoids, polysaccharide, betaine, and yield.