The invention provides an application of single cell sequencing in immune cell analysis. The immune cells comprise any one or a combination of at least two of T cells, mononuclear cells, natural killer cells, B cells, macrophages, granulocytes, mast cells, megakaryocytes or dendritic cells. Wherein the immune cell analysis comprises analysis of any one or a combination of at least two of types, states or proportions of immune cells and / or immune cell subtypes. In the present invention, single cell sequencing is applied to the immune cell analysis, a method comprises the following steps: firstly, obtaining a sequencing result of a sample through single cell sequencing, then obtaining a distribution state, subtype composition and a cell track of immune cells by adopting a biological information analysis method, annotating the cell subtypes, and realizing analysis on the types, states and proportions of the immune cells and / or the immune cell subtypes by comparing different results.