Van der Waals heterostructures offer attractive opportunities to design quantum materials. For instance, transition metal dichalcogenides (TMDs) possess three quantum degrees of freedom: spin, valley index and layer index. Furthermore, twisted TMD heterobilayers can form moire patterns that modulate the electronic band structure according to the atomic registry, leading to spatial confinement of interlayer excitons (IXs). Here we report the observation of spin-layer locking of IXs trapped in moire potentials formed in a heterostructure of bilayer 2H-MoSe2 and monolayer WSe2. The phenomenon of locked electron spin and layer index leads to two quantum-confined IX species with distinct spin-layer-valley configurations. Furthermore, we observe that the atomic registries of the moire trapping sites in the three layers are intrinsically locked together due to the 2H-type stacking characteristic of bilayer TMDs. These results identify the layer index as a useful degree of freedom to engineer tunable few-level quantum systems in two-dimensional heterostructures. The optical properties of two species of localized interlayer excitons in a van der Waals heterostructure are shown to depend on their spin-valley-layer configuration, enabling the identification of the moire atomic registry and offering insights for engineering quantum states in two-dimensional materials.