This paper investigates the impact of alignment between the target function of interest and the kernel matrix on a variety of kernel-based methods based on a general loss belonging to a rich loss function family, which covers many commonly used methods in regression and classification problems. We consider the truncated kernel-based method (TKM) which is estimated within a reduced function space constructed by using the spectral truncation of the kernel matrix and compare its theoretical behavior to that of the standard kernel-based method (KM) under various settings. By using the kernel complexity function that quantifies the complexity of the induced function space, we derive the upper bounds for both TKM and KM, and further reveal their dependencies on the degree of target-kernel alignment. Specifically, for the alignment with polynomial decay, the established results indicate that under the just-aligned and weakly-aligned regimes, TKM and KM share the same learning rate. Yet, under the strongly-aligned regime, KM suffers the saturation effect, while TKM can be continuously improved as the alignment becomes stronger. This further implies that TKM has a strong ability to capture the strong alignment and provide a theoretically guaranteed solution to eliminate the phenomena of saturation effect. The minimax lower bound is also established for the squared loss to confirm the optimality of TKM. Extensive numerical experiments further support our theoretical findings.