The invention provides a method for cell quality control through unicellular transcriptome sequencing. The method comprises the following steps of: performing unicellular separation so as to obtain a total unicellular number; performing transcriptome amplification on each unicell; confirming that amplification can be implemented but the unicellular number is not sufficient for analysis on sequencing results; performing sequencing and analysis, including performing main component analysis and cluster analysis on the sequencing results, comparing with a standard unicellular database, and calculating the unicellular number off from total tendency; screening, including screening based on unicellular partitioning and screening based on expression gene types, wherein the step of screening based on unicellular partitioning comprises a step of screening cells of which the activity levels are greater than 75%, and the step of screening based on the expression gene types comprises a step of classifying expression genes into a good gene group, a neutral gene group and a malignant gene group according to gene functions. By adopting the method provided by the invention, the uniformity or the homogeneity of cells can be effectively controlled.