In this work, a microwell-chip was prepared and modified. The microwell-chip was used for extraction of metabolites and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry (ESI-MS) was adopted for metabolome identification and a data independent acquisition (DIA)-MS approach was established for simultaneous proteome profiling and phosphoproteome analysis. In particular, application of this strategy provides a multi-omics view of cellular changes.