The development of high-throughput screening methods for microorganisms is desired because microorganisms are useful and sustainable resources with which valuable substances utilized in various industries can be produced. Micro-space-based methods are the best candidates for the efficient screening of microorganisms owing to their low reagent consumption and compact integration. In this study, we developed a picoliter-sized incubator array for quantitative and labeling-free evaluation of the growth process of Escherichia coli (E. coli) by autofluorescence. Because the array with 8464 incubators is able to compartmentalize single E. coli individually utilizing the Poisson distribution, the array can evaluate 100 single E. coli simultaneously. Our incubator array not only realized the high-throughput screening of microorganisms, but also provided an analytical tool for assessing individual differences in E. coli.