In cotton production, drought is particularly prominent in the flowering and boll formation stage, which significantly affects the cottonseed yield and quality. As the two main storage products in cottonseed kernel, the formation of oil and protein will be affected inescapably under soil drought. Still, the effects of soil drought on the synthesis of cottonseed oil and protein are poorly investigated. To this end, experiments were conducted using two cultivars with contrasting drought tolerance (Dexiamian 1 and Yuzaomian 9110) under three water levels [soil relative water content: control (75 ± 5)%, mild drought (60 ± 5)% and severe drought (45 ± 5)%] from 2017 to 2019. We examined the responses of metabolic activities in cottonseed kernels to drought. Otherwise, 13 CO 2 and 15 N-urea isotope labeling were applied to verify the trend of oil and protein accumulation under soil drought. Results showed that drought decreased cottonseed yield per plant due to the decreases of single-seed weight and cottonseed number. And drought decreased oil content (% dry weight −1 ) and increased protein content (% dry weight −1 ) in cottonseed kernel. According to the findings, drought decreased 13 C content and limited the flow of carbon into oil synthesis pathway; moreover, drought decreased the expression of GhPEPC1 and GhDGAT and activities of phosphoenolpyruvate carboxylase (PEPCase) and diacylglycerol acyltransferase (DGAT), which restrained oil accumulation. Increased protein content under drought was attributed to the increased translocation of plant nitrogen to cottonseed kernel, higher expression of GhGS and GhGOGAT , glutamine synthetase (GS) and glutamate synthase (GOGAT) activities. The Yuzaomian 9110 was more sensitive to drought stress with a higher loss of cottonseed yield and yield components than Dexiamian 1. This study provides insight into the physiological mechanisms of cottonseed oil and protein synthesis under drought and provides a theoretical basis for the utilization of cottonseed oil and protein in the future. Annotation: PEP, phosphoenolpyruvic acid; OAA, oxaloacetic acid; TCA, tricarboxylic acid cycle; Ace-CoA, acetyl coenzyme A; Mal-CoA, Malonyl mono-CoA; G3P, glyceraldehyde 3-phosphate; DAG, diacylglycerol; TAG, triacylglycerol; NADPH, nicotinamide adenine dinucleotide phosphate; PEPCase, Phosphoenolpyruvate carboxylase; ACCase, acetyl-CoA carboxylase; DGAT, diacylglycerol acyltransferase; GS, glutamine synthetase; GOGAT, glutamate synthase; AST, aspartate aminotransferase; ALT, alanine aminotransferase. • Cottonseed yield was significantly decreased under soil drought. • Drought stress significantly restrained 13 C into oil in cottonseed kernels, and enhanced 15 N into kernels. • The oil content was restrained under drought due to lower carbon substrates and enzyme activities. • The increase of nitrogen accumulation and protein synthesis enhanced kernel protein content under drought.