Pulsed direct current electrospray ionization mass spectrometry (PDESI-MS) offers many advantages such as in situ, real-time, fast, and microvolume sample analysis. However, the current PDESI-MS system requires manual operation for sample processing and mass spectrometry injection, which have many disadvantages such as cumbersome operation, many steps, large errors and low accuracy. Herein, a high-throughput, fully automated and integrated PDESI-MS system was developed, and an in situ detection for small molecule metabolites in eukaryotes (single bladder cancer cells) and prokaryotes (single colonies of bacteria) was explored. The results showed that the automated PDESI-MS system could effectively detect metabolites of different strains and realize the classification and stereotyping of different types of Escherichia coli. In addition, the picoliter droplet generation technology allowed it to be applied to single cell detection. The automated PDESI-MS system could achieve high precision, high density, high repeatability and high automation for in situ sample extraction, especially in detection and analysis of small samples, and showed great application potential and development prospects in food safety, regenerative medicine, drug screening, clinical treatment and other fields.