Stylo has a great potential for Al3+ resistance in acidic soils through secretion of citrate from the roots. To get insight into the molecular mechanisms responsible, transcriptomic changes were investigated in the roots after treatment with T01 (-Al3+, pH6.0), T02 (-Al3+, pH4.3) and T03 (50 µM AlCl3, pH4.3). In total, 83,197 unigenes generated from 130,933 contigs were obtained. Of them, 282, 148 and 816 differentially expressed unigenes (DEGs) were revealed in T01_vs_T02, T02_vs_T03 and T01_vs_T03 comparison, respectively (FDR < 0.001, log2FC > 2). DEGs by Al3+ were related to G-proteins, diacyglycerol and inositol metabolism, calcium-signaling, transcription regulation, protein modification and transporters for detoxification of Al3+. Additionally, Al3+ facilitates citrate synthesis via modifying gene expression of pathways responsible for citrate metabolism. Overall, Al3+ resistance in stylo involves multiple strategies and enhancement of citrate anabolism. The Al3+ signal transmits through heterotrimeric G-proteins, phospholipase C, inositol triphosphate, diacylglycerol, Ca2+ and protein kinases, thereby activating transcription and anion channels in plasma membrane, and resulting in citrate secretion from stylo roots.