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 moiré 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 moiré 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 moiré 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.