Previous research results show that the conductance difference in molecular junction caused by quantum interference (QI) effect is an important way to identify isomers or improve the recognition sensitivity. Recently, single-molecule conductance of two fully π-conjugated dithienoborepin (DTB) isomers (DTB-A and DTB-B) with tricoordinate boron centers has been measured by using the scanning tunneling microscopy break junction technique. The result shows that QI can enhance chemical responsivity in single-molecule DTB junction. In this work, the first-principles method based on density functional theory and non-equilibrium Green's function is used to study the influence of QI effect on spin-transport property of DTB molecular junction connected to the nickel electrode, and the purpose of distinguishing DTB isomers (DTB-A and DTB-B) is realized by using amino and nitro passivation. The results show that the pristine DTB-A molecule and DTB-B molecule both have a up-spin transmission peak dominated by HOMO and a down-spin transmission peak dominated by LUMO on both sides of the Fermi level, and the energy positions and coefficients of two transmission peaks are basically the same. Therefore, the up-spin and down-spin current curves of the two junctions basically coincide, so that it is impossible to clearly distinguish the two isomers of DTB molecule simply by spin current. The QI can enhance the spin-polarized transport capability of two orbitals of amino-passivated DTB-A molecule to varying degrees but weaken the spin-polarized transport capability of two orbitals of amino-passivated DTB-B molecule. Therefore, the current of DTB-A molecular junction passivated by amino group is always higher than that of DTB-B molecular junction passivated by amino group. However, the QI can greatly enhance the spin-polarized transport capability of two orbitals of nitro-passivated DTB-B molecule but weaken the spin-polarized transport capability of two orbitals of nitro-passivated DTB-A molecule. Therefore, the current of DTB-B molecular junction passivated by nitro is always higher than that of DTB-A molecular junction passivated by nitro. Because the QI has different effects on the spin-transport capability of DTB-A and DTB-B passivated by amino or nitro group, so the two isomers of DTB molecule can be distinguished by measuring the spin current value. The above conclusions provide more theoretical guidance for the practical preparation of spin molecular junctions and the regulation of their spin-transport performance in the future.