The post-encapsulation method (such as single-layered encapsulation) is a promising strategy to synthesize yolk-shell structures that protect functional nanoparticles by the molecular sieving effect. However, this method exhibited limited loading capacity and nonuniform encapsulation during the co-encapsulation of various nanoparticles owing to the insufficient surface area for nanoparticle attachment. To address these limitations, we proposed a double-layered encapsulation method comprising an increased number of silica template layers and separate attachment of multifarious nanoparticles to different layers. Compared with conventional methods, this strategy can precisely adjust the ratio of encapsulated nanoparticles and increase the loading amount, which improves the functionality of yolk-shell structures, such as the photothermal properties of gold nanoparticle-encapsulated yolk-shell structures (∼69%). We describe, for the first time, the precise control of the ratio of encapsulated nanoparticles and the loading of numerous nanoparticles. Consequently, this strategy has significant potential for various applications of yolk-shell structures.