Numerous crystals and Frank-Kasper phases in two-dimensional (2D) systems of soft particles have been presented by theoretical investigations. How to realize 2D crystals or Frank-Kasper phases via the direct self-assembly of three-dimensional (3D) systems remains an important issue. Here, through numerical simulations, we report the surprising finding of multiple 2D crystal structures in bilayered lamellae from the direct self-assembly of 3D systems of soft Janus particles. With varying the patch size and particle density, soft Janus particles, which exhibit very similar self-assembly behavior to giant amphiphiles, spontaneously form ordered bilayered lamellae. Within each layer of the bilayered lamellae, we find abundant highly-ordered 2D crystals including the Frank-Kasper σ phase and open kagome lattice. The kinetic mechanisms of the formation of these 2D crystals within the layers are revealed, and include a classical one-step nucleation mechanism and a two-step nucleation mechanism. Our findings suggest a simple route towards 2D crystals via the direct self-assembly of 3D systems of amphiphilic Janus building blocks.