Anderson Fabry disease (AFD) is caused by mutations in the X-linked gene GLA, encoding lysosomal enzyme α-galactosidase A (α-GAL). The gene mutations reduce the enzymatic activity, resulting in significant lysosomal accumulation of enzyme substrates glycosphingolipids, mainly globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3). However, how the accumulated glycosphingolipids cause disease phenotypes remain largely unknown. Here, we employed human induced pluripotent stem cells (iPSCs) modified with clustered regularly interspaced short palindromic repeats interference (CRISPRi) to model cardiac AFD in vitro. We found that clumps of iPS-derived cardiomyocytes (iPS-CMs) with CRISPRi-mediated GLA knockdown exhibited impaired beating, prolonged Ca²⁺ decay and relaxation. Mechanistically, α-GAL reduction increased unphosphorylated PLN by perturbing mTOR (specifically mTORC2, but not mTORC1)-AKT signaling. These results reveal how the pathogenic glycosphingolipids intersect with the mTORC2-AKT-PLN axis regulating relaxation and impair it, leading to the cardiac abnormalities. Our study reinforces the usefulness of the CRISPRi iPSCs in modeling monogenic diseases and delineating mechanisms of the diseases.