The strategy of MOFs functionalization by modifying ligands is a powerful platform among other ongoing researchs which is creating high-performance MOFs. Ligands modification through the addition of support groups (in helping of host–guest main interaction sites) has a key role in the increasing of host molecule adsorption capacity. To investigate this issue we synthesized two structures TMU-59 and TMU-6(RL1) and studied the effect of MOFs functionalization with functional groups such as methyl group in the vicinity of basic amine groups on the detection of guest molecules. The sensing ability of TMU-6(RL1) as parent structure and methyl functionalized TMU-59 has studied for the detection of TNP in aqueous solutions. Our results reveal that the insertion of methyl groups on pillaring linker can remarkably increase the hydrophobicity, stability and electron density of MOFs as well as maximizing the interaction with the nitro-aromatics guests by providing multiple adsorption mechanisms such as hydrogen bonds and π-π interactions. The detection limit for TNP in water solvent is 0.46 and 102 ppb for TMU-59 and TMU-6(RL), respectively. Present work as a comprehensive study reveals that how MOFs functionalization through the addition of relatively active group such as methyl would have influenced the overall sensing behavior.