This paper describes a rational strategy to obtain self-assembled two-dimensional (2D) nanocrystals with definite and uniform thickness from a series of molecular Janus particles based on molecular nanoparticles (MNPs). MNPs are 3D framework with rigid shapes. Three different types of MNPs based on derivatives of polyhedral oligomeric silsesquioxane (POSS), [60]fullerene (C-60), and Lindqvist-type polyoxometalate (POM) are used as building blocks to construct these amphiphilic molecular Janus particles by covalently connecting hydrophobic crystalline BPOSS with a charged hydrophilic MNP. The formation of 2D nanocrystals with an exact thickness of double layers of molecules is driven by directional crystallization of the BPOSS MNP and controlled by various factors such as solvent polarity, number of counterions, and sizes of the MNPs. Strong solvating interactions of the ionic MNPs in polar solvents (e.g., acetonitrile and dimethylformamide) are crucial to provide repulsive interactions between the charged outlying ionic MNPs and suppress further aggregation along the layer normal direction. The number of counterions per molecule plays a major role in determining the self-assembled morphologies. Size matching of the hydrophobic and ionic MNPs is another critical factor in the formation of 2D nanocrystals. Self-assembly of rationally designed molecular Janus particles provides a unique "bottom-up" strategy to engineer 2D nanostructures.