The precise generation of diverse neuronal cell types is crucial for normal brain function. Genetic mutations leading to impaired neuronal development have long been linked to neurodevelopmental disorders. Cerebral organoids can be used to investigate neurodevelopmental disorders in a human context but are limited by variability and low throughput. We have developed the CRISPR-human organoids-scRNA-seq (CHOOSE) system that utilizes verified pairs of gRNAs, inducible CRISPR/Cas9-based genetic disruption, and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Genetic perturbations of 36 high-risk autism spectrum disorder (ASD) genes related to transcriptional regulation allowed us to identify their effects on cell fate determination and discover developmental stages susceptible to ASD gene perturbations. We show that perturbing members of the BAF chromatin remodeling complex leads to an expanded population of ventral telencephalon progenitors. Specifically, the BAF subunit ARID1B controls the fate transition of progenitors to oligodendrocyte precursor cells and interneurons, which we confirmed in patient-specific induced pluripotent stem cell (iPSC) derived organoids. The CHOOSE system provides a robust, precisely controlled screening strategy to identify cell type-specific contributions to genetic disorders. Moving forward, the CHOOSE system has the potential to be utilized for investigating more intricate, human-specific processes in brain development and exploring the roles of disease-associated genes in various contexts.