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• Modified biochar decreased pH of salt-affected soils in an intercropping system. • Oversupply of biochar had negative impact on soil water and crop yield. • A 10 t ha−1 biochar application rate was recommended to improve soil and yields. Biochar application in agricultural salt-affected soils has shown strong potential to amend soil and promote production. The effect of biochar on soil properties and crop yield varies with crop, soil, biochar properties and climate. Thus, it is critical to select suitable biochar and their application amounts for ameliorating salt-affected soils while improving its conditions and crop yields. The objectives of this study were to investigate the effect of biochar application rates on soil properties, water and temperature conditions and crop yields in saline-alkali soils under cotton-sugarbeet intercropping. We used a three-year (2018–2020) field experiment with biochar application rates of 0, 10, 50 and 100 t ha−1 in 2018, 0, 10, 25, 50 and100 t ha−1 in 2019 and 0, 10, 25 and 30 t ha−1 in 2020. Soil bulk density decreased and thus porosity increased with application of biochar. Soil pH decreased with increasing biochar application amount and the rate of change ranged from −0.003 to −0.004 per ton of biochar. Biochar application at 10 t ha−1 increased soil water content (SWC) and weighted planar soil water storage (WPSWS) in all three experimental years, while oversupply of biochar decreased SWC. Application of biochar moderated soil temperature fluctuations. The yield of cotton and sugarbeet first increased and then decreased with increasing amount of biochar. Considering the effects of biochar on soil water, temperature, and crop yields, 10 t ha−1 biochar amount was proposed as an appropriate application rate for saline-alkali soils. The results provided valuable information on appropriate biochar rates to amend salt-affected soils and their properties while increase crop yields. [ABSTRACT FROM AUTHOR]