In this paper, an unstable chiral drug L-alanyl-glutamine (L-(Ala-Gln)) was intercalated into layered double hydroxides (LDHs) and a systematic study combining experimental and theoretical investigation was carried out. Structural characterization reveals the microstructure of LDHs and properties of the intercalated L-(Ala-Gln). Solid-state UV-vis spectroscopy is adopted to observe the energy absorption. This result shows that LDHs can block the UV light, and inhibition of configuration conversion works in the LDH host. Circular dichroism (CD) spectra suggest that the intercalated L-(Ala-Gln) can maintain its configuration in the interlayer even when irradiated under UV light. Density functional theory (DFT) computations at the B3PW91/6-31G(d, p) level have been carried out to understand the mechanism of L-(Ala-Gln) racemization. The computed result demonstrates that the thermal energy based on the reaction temperature cannot support L-(Ala-Gln) to give an excited state, but it can be excited under the irradiation of UV light with a wavelength less than 240 nm and undergoes conformational transition. When intercalated in the interlayer of LDHs, L-(Ala-Gln) is involved in strong guest-host interaction with the layers and thus inhibition of configuration conversion is effective in the LDH interlayer.