Tuberous sclerosis complex (TSC) is a genetic disorder characterized by tumor formation in multiple organs, with over 80% of TSC patients developing angiomyolipomas (TSC-AMLs). However, the molecular events that contribute to TSC-AMLs are not well understood. Recent reports have demonstrated that microRNAs (miRNAs) are critical in TSC cortical tubers. However, little is known about the role of miRNAs in TSC-AMLs. In the current study, we analyzed changes in the miRNA and mRNA profiles in TSC-AMLs and matched normal adjacent tissues. A total of 15 differentially expressed miRNAs and 2664 mRNAs were identified. Using quantitative real-time PCR, we confirmed the results of the miRNA and mRNA profile experiments. Through bioinformatic analysis and luciferase reporter assays, we found that BCL2L11, an apoptotic activator, was the direct target of miR-9-5p, miR-124-3p, and miR-132-3p. Engineered expression of miR-9-5p, miR-124-3p, or miR-132-3p significantly regulated proliferation and apoptosis in Tsc2-/- cells. Manipulated expression of BCL2L11 also led to proliferation and apoptosis alterations in Tsc2-/- cells, in agreement with the effects of the above three miRNAs. In addition, BCL2L11 rescued the proliferation and apoptotic inhibition induced by miR-9-5p, miR-124-3p, and miR-132-3p in Tsc2-/- cells. This study provides supportive evidence that miR-9-5p, miR-124-3p, and miR-132-3p play a role in TSC-AMLs through the regulation of BCL2L11.