Saccharomyces cerevisiae (S. cerevisiae) is well-known as baker's yeast and brewer's yeast in the food industries and also used as a probiotic in humans. It has been classically considered as a safe non-pathogenic organism, but the number of cases about its implication as an etiologic agent of invasive infections has been increasing in the last two decades. Furthermore, it is difficult to achieve timely diagnosis and early prevention of the related infections in clinical due to long-time being sped in isolation and detection of S. cerevisiae. Here, we propose a novel method of label-free rapid detection of invasive S. cerevisiae infections with a coupled system of optically induced dielectrophoresis (ODEP)-based micromanipulation and graphene transistor. The S. cerevisiae was quickly separated and isolated from its surroundings by ODEP-based micromanipulation, and its optimal operating conditions were experimentally evaluated to quickly collect S. cerevisiae with higher purity (up to 99%) and larger collection rate (more than 65%). The property of S. cerevisiae was detected accurately by the graphene transistor through two measurement modes. And the results validated the graphene transistor obviously distinguish the different concentrations of the S. cerevisiae, characterized by conductance changes or I-V curves of the graphene transistor. This work represents a step toward the use of the coupling of micromanipulation and nanosensor to realize the integrated isolation and detection of S. cerevisiae. Furthermore, it also has potential as a novel approach of isolation and detection of other organisms for the microbiological research and detection of fungal infections.