2D-layered transition metal chalcogenides are useful semiconductors for a wide range of opto-electronic applications. Their similarity as layered structures offers exciting possibility to modify their electronic properties by creating new heterojunction assemblies from layer-by-layer restacking of individual monolayer sheets, however, the lack of specific interaction between these layers could induce phase segregation. Here, we employed a chemical method using n-BuLi to exfoliate MoS₂ and In₂Se₃ into their monolayer-containing colloids in solution. The bulky Se atoms can be selectively leached from In₂Se₃ during Li treatment which gives positively charged surface monolayers in neutral pH whereas the strong polarization of Mo–S with moderate S leaching gives a negatively charged surface. Specific interlayer electrostatic attraction during their selective assembly gives a controllable atomic AB-type of layer stacking as supported by EXAFS, STEM with super-EDX mapping, TAS/TRPL and DFT calculations. Using this simple but inexpensive bottom-up solution method, a new photocatalyst assembled from layers for photo water splitting can be tailor-made with high activity.