The penicillinase enzyme plays an important role in local ecological efficiency and resistance to antibiotic agents. Bacillus licheniformis, the causative agent of septicemia, has a high penicillinase activity. The main goal of this study was to identify selective inhibitors for clinical applications. To achieve this, the inhibitory effects of four chemical compounds on the activity of the Bacillus licheniformis (B. licheniformis) penicillinase enzyme were evaluated. B. licheniformis PTCC 1320 (NCIB6346) was cultured in tryptic soy broth (TSB) (30 g/L) liquid culture medium and was adjusted to 0.5 McFarland turbidity standard (4-hr culture). Mueller-Hinton broth (MHB) was used to adjust the turbidity. Then, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of benzylpenicillin antibiotic (penicillin G) were determined. Then, a concentration of 8 mg/ml of citrate was chosen and consistently added to all the tubes (serial tubes). Enzyme inhibition by Citra and other inhibitors was evaluated by measuring MIC and MBC in the presence of each compound separately. Finally, the results were confirmed by molecular modeling data. The MIC and MBC levels of benzylpenicillin were determined to be 2 and 4 μg/mL, respectively. However, in the presence of citrate, the MIC and MBC values of benzylpenicillin were found to be 0.125 and 0.25 μg/mL, respectively. Moreover, molecular docking results showed that the active site of penicillinase had an anionic cavity where amino acid anions (Thr 235, Arg 24, Ser 70, Ser 130, Tyr 135, Asn 170, and Asn 104) were present and stabilized the intermediates formed in this site by inducing electrostatic interactions. Citrate could competitively attach to this site. The other three compounds (diethyl malate, malic anhydride, and malic acid) showed similar binding patterns to citrate, but were smaller in size and had fewer active groups: their interactions were less strong and weaker than those of citrate can enhance ecological efficiency. The results show that citrate is the best inhibitory compound for B. licheniformis penicillinase as well as for promoting ecological construction.