Layered transition metal chalcogenide nanostructures reveal unprecedented electronic and optical properties due to the unusual arrangement of interlayers and electronic interactions between them. Here, we report layered FeSe nanoparticles (NPs) coupled by L- or D-cysteine as a chiral stabilizer to show multi-colored excitation dependent emission (MEDE) for both single- and two-photon photoluminescence breaking conventional Kasha and Vavilov rules of luminescence, which is the first report in inorganic nanostructure system. Structural analysis shows the chiral stabilizer-induced interlayer spacing expansion in a FeSe NP. The MEDE in FeSe NPs is revealed to originate from the impurity coupled to the Mott insulator character of FeSe and chiral interlayer expansion through the first-principles electronic structure calculations and the classical molecular dynamics. Taking advantage of biocompatibility and multiphoton excitation in FeSe NPs, MEDE was utilized for bio-imaging of neuron cells and tissues altering excitation wavelength from visible to near-infrared range expanding the capabilities of multi-color bio-labeling.