Purpose – The purpose of this paper is to find the reason which the results of grey variable weight clustering method do not correspond with the reality. It proposes reconstructing the whitenization weight function, outlining why and how inconsistency is avoided. The study aims to improve the model of grey clustering method based on the whitenization weight function and list the steps of the new clustering model so that analysis and application of innovation capacity in a broader range is normally found. Design/methodology/approach – First the reason for the problem that the clustering results of grey variable weight clustering do not correspond with the reality is analyzed in two existing literature. And then a new whitenization weight function is reconstructed, two properties of the whitenization weight function are proved. The solution of the new grey variable weight clustering based on the whitenization weight function is built by following six steps. Findings – The paper provides a new whitenization weight function which satisfies the normative and non-triplecrossing. It suggests that successful clustering results of innovation capacity act on two levels: integrating the elements of innovation capacity indexes, and following steps of grey variable weight clustering. Originality/value – This paper improves the existing method of grey variable weight clustering and fulfills an identified need to study how cities’ innovation capacity can be clustered.