Morphologic and genetic alterations play crucial roles in tumorigenesis, and are the foundation of diagnosis in cancer research. However, visualization of tumor morphology often requires staining which compromises the genetic material, making the interpretation of genetic alterations a challenge. Histological staining is especially detrimental when measuring the transcriptomic changes that underlie variation of histological features at the microscopic level. Here we propose stimulated Raman scattering micro-dissection sequencing (SMD-Seq), which exploits the intrinsic vibrational signatures of chemicals to rapidly construct label-free histological images of cryo-sectioned tissues, and achieves in situ laser micro-dissection of small regions of interest for location-specific and simultaneous transcriptome and genome analysis. We applied SMD-Seq to unstained cryosections of human oral squamous cell carcinoma (OSCC) samples. SRS images proved to be comparable to H&E staining in revealing the morphological characteristics of tissues, and capable of differentiating the small cancer regions from normal epithelium of OSCC. With significantly reduced nucleic acid loss, accurate identification of copy number variations, gene expression levels, and gene-fusion events were obtained through genome and transcriptome analysis of SRS-guided high-purity micro-dissected regions. The high-resolution histological characteristics combined with preservation of high quality genetic material from specific regions of interest enabled the characterization of inter- and intra-tumor heterogeneity using morphological and genetic analysis. Given histopathological features and matched biomolecular content, SMD-Seq provides complementary insights in the study of cancer, and opens a window for correlative analysis between morphology and genome and transcriptome sequencing in complex samples with intrinsic genetic mosaicism.