Aiming at the disadvantages of the traditional direct of targets sequencing which neglects uncertainties and opposing factors, put forward the index system of artillery long-rang accurate attack targets sequencing according to set pair analysis theories. To find relations between the certainty and uncertainty of the system through its 3 aspects: the same, the different, and the opposite. Use the link degree on all situations to deal with the targets sequencing based on the set pair analysis and give an example at last. The results show that the approach is simple, novel, easy to programming and suitable for handing large amounts of date, it can better solve the problem of analytic deviation with qualitative analysis.