The invention relates to the technical field of gene engineering, in particular to a chlorella vulgaris chloroplast homologous recombinant empty vector and application thereof. The recombinant empty vector comprises upstream and downstream homologous arms, at least one promoter and at least one terminator are arranged between the upstream and downstream homologous arms, and a base sequence which is as shown in SEQ ID NO: 7 and forms a polycistron structure with at least one exogenous gene is inserted between the promoter and the terminator; and the upstream homologous arm contains a base sequence shown as SEQ ID NO: 1, and the downstream homologous arm contains a base sequence shown as SEQ ID NO: 2. By adopting a chlorella vulgaris chloroplast stable expression system disclosed by the invention, stable expression of a plurality of exogenous genes in chloroplast can be realized.