The cosine router in Mixture of Experts (MoE) has recently emerged as an attractive alternative to the conventional linear router. Indeed, the cosine router demonstrates favorable performance in image and language tasks and exhibits better ability to mitigate the representation collapse issue, which often leads to parameter redundancy and limited representation potentials. Despite its empirical success, a comprehensive analysis of the cosine router in MoE has been lacking. Considering the least square estimation of the cosine routing MoE, we demonstrate that due to the intrinsic interaction of the model parameters in the cosine router via some partial differential equations, regardless of the structures of the experts, the estimation rates of experts and model parameters can be as slow as $\mathcal{O}(1/\log^τ(n))$ where $τ> 0$ is some constant and $n$ is the sample size. Surprisingly, these pessimistic non-polynomial convergence rates can be circumvented by the widely used technique in practice to stabilize the cosine router -- simply adding noises to the $\ell^2$-norms in the cosine router, which we refer to as \textit{perturbed cosine router}. Under the strongly identifiable settings of the expert functions, we prove that the estimation rates for both the experts and model parameters under the perturbed cosine routing MoE are significantly improved to polynomial rates. Finally, we conduct extensive simulation studies in both synthetic and real data settings to empirically validate our theoretical results.