Developmental signals and environmental stresses regulate carbon distribution in the vegetative and reproductive organs of plants and affect seed yield. Cleistogenes songorica is a xerophytic grass with great potential application value in ecological restoration. However, how carbohydrate transport and distribution during grain filling affect the seed yield of C. songorica under water stress is not clear. The present study showed that the soluble sugar and starch contents of cleistogamous (CL) spikes and chasmogamous (CH) spikes were significantly higher at the milk stage, which was attributed to a significantly higher seed number and seed yield per spike under water stress conditions than under well-watered conditions (P < 0.01). RNA-seq data revealed a total of 54,525 differentially expressed genes (DEGs) under water stress conditions, but only 3744 DEGs were shared among all comparison groups. Weighted gene co-expression network analysis showed that the transport and distribution of carbohydrates were regulated by ABA-responsive genes (CsABA8OX1_1, CsABA8OX1_2, CsABA8OX2_1, CsABA8OX2_2, CsNCED3, CsNCED1_1, CsNCED1_2 and CsNCED4_1) and sugar transport and starch synthesis genes (CsSUS1, CsSUS2, CsSUS3, CsAGP1, CsAGP4, CsAGP5, CsSSS1 and CsSBE5) under water stress conditions. These genes jointly regulated carbohydrate remobilization in sources (stems, leaves and sheaths) to promote grain filling and improve seed yield. The present study helped to clarify the phenotypic, metabolic and transcriptional response mechanisms of vegetative organs, such as stems and leaves, and reproductive organs, such as CL spikes and CH spikes, to promote carbohydrate redistribution under water stress, and it provides theoretical guidance for improving seed yields.