Single cell analysis is a powerful tool to unveil cell heterogeneity, which may play a important role in series events in cancer progression, such as tumor initiation, metastasis and clinical chemotherapy resistance. To profile subtle biological variations at individual cell level, methods that allows single cell imaging and corresponding gene expression are still urgently required. Here, we adapted previously developed microfluidic techniques for massive single cell imaging and implemented this strategy to conduct single cell apoptosis analysis and followed by picking up individual cells from the micro-well, performing single cell RNA sequencing, to gain single cell imaging and RNA sequencing data correspondingly. We utilized drug resistant breast cancer cell line and wild type to demonstrate the capability of this approach, which can realize thousands of single cell apoptosis analysis and single cell RNA-seq at the very interested individual cells. From images to corresponded single cell gene expression data, the multiple drug resistant genes has been validated as the main contributors to the phenotype of doxorubicin resistance.