We consider the following prescribed curvature problem involving polyharmonic operators on \(\mathbb {S}^{N}\) \(\begin{aligned} D^{m}{\tilde{u}} = \widetilde{K}(y){\tilde{u}}^{m^{*}-1}, \quad {\tilde{u}} > 0 \ \hbox { in } \mathbb {S}^{N}, \quad {\tilde{u}} \in H^{m}(\mathbb {S}^{N}), \end{aligned}\) where \(\widetilde{K}(y)>0\) is a radial function, \(m^{*}=\frac{2N}{N-2m}, m\ge 1\) is an integer and \(D^m\) is 2m-order differential operator given by \(\begin{aligned} D^m=\prod _{i=1}^m \bigg (-\Delta _g+\frac{1}{4}(N-2i)(N+2i-2)\bigg ). \end{aligned}\) Here \(\Delta _g\) is the Laplace-Beltrami operator on \(\mathbb {S}^N\) , and \(\mathbb {S}^N\) is the unit sphere with Riemann metric g. We are concerned with the solutions which are invariant under some non-trivial sub-group of \(\mathcal {O}(3)\) to the above problem. We first prove a non-degeneracy result for this kind of \(\mathcal {O}(3)\) invariant solutions. As an application, we consider an eigenvalue problem, we investigate the properties of the eigenvalues and obtain the Morse index estimate of the \(\mathcal {O}(3)\) invariant solutions. Our proof is based on the local Pohozaev identities, blow-up analysis, and the properties of the Green function.