Background: Detecting the complete transcriptome, including polyadenylated and nonpolyadenylated RNA, is crucial for understanding cellular roles. However, current efforts to investigate the total cellular transcriptome in single cells are limited by the lack of an automated, high-throughput assay. We developed scComplete-seq, a method that enhances existing droplet-based single-cell mRNA sequencing to provide insights into the nonpolyadenylated transcriptome. This method allows us to detect long and short nonpolyadenylated RNAs at single-cell resolution. Applying this method to peripheral blood mononuclear cells (PBMCs), we discovered unique patterns of tRNA and snRNA associated with cellular subtypes and their dynamic changes in response to different stimuli. Moreover, enhancer RNAs could be simultaneously profiled with mRNA in this method, providing important insights into the transcriptional regulation. Single-cell Complete RNA sequencing (scComplete-seq) is a versatile technology that can readily enable the exploration of the comprehensive transcriptome at single-cell resolution for various applications.