This paper investigates the critical role of eigenalignments between the kernel matrix and learning targets in achieving robust generalization in learning problems. We establish a direct connection between generalization performance in kernel methods and the estimation of eigenvectors and eigenvalues of matrices, offering a more intuitive understanding compared to prior work with minimal assumptions. We also show that, since the prediction task in KRR is essentially the weighted sum of eigenvectors/singular vectors, by analyzing how much error can be caused by perturbations to the kernel matrix, we can then derive a bound on this generalization error using the estimation stability of matrix eigenvalues and eigenvectors. Compared with previous work, our analysis concentrates on finite-sample settings and on the generalization error arising from having a suboptimal finite training set. Our findings reveal that in kernel methods, as long as the kernel is of high rank, the near-zero reconstruction error can be trivially obtained, implying that the reconstruction error will have limited predictive power for generalization. Finally, we establish a generalization bound from an eigenvalues/eigenvectors estimation perspective, showing that strong generalization requires increasing eigenvector alignment, eigenvalue magnitude, or gaps between consecutive eigenvalues.