Two Zn-MOFs, namely, {[Zn(L)0.5(bpea)]·0.5H2O·0.5DMF}n [LCU-113 (for Liaocheng University)] and {[Zn(L)0.5(ibpt)]·H2O·DMF}n (LCU-114), were synthesized based on flexible tetracarboxylic acid 1,3-bis(3,5-dicarboxyphenoxy)benzene (H4L) and different N-ligands [bpea = 1,2-dipyridyl ethane; ibpt = 3-(4'-imidazolobenzene)-5-(pyridine-4'-yl)-1,2,4-triazole]. LCU-113 and LCU-114 possess twofold interpenetrating three-dimensional pillared layer structures, in which a two-dimensional layer formed by carboxylic acid and Zn2+ ions was pillared by bpea and ibpt, respectively. The two complexes show high water stability and high luminescence sensing performance toward organic solvents, ions, and antibiotics, as well as chemicals, in simulated urine. The investigation showed that (1) LCU-113 and LCU-114 could detect uric acid (UA, 2,6,8-trihydroxypurine, metabolite of purine) and p-aminophenol (PAP, biomarker of phenamine) in simulated urine by luminescence quenching, respectively, and (2) luminescence quenching of LCU-113 and LCU-114 occurred in aqueous solutions of nitrofurazone (NZF), Fe3+, and CrO42-/Cr2O72-. All the above detections have excellent anti-interference ability and recyclability. The luminescence mechanism analysis indicates that weak interactions between the framework structures and the target analytes as well as the energy competition (inner filter effect) play an important role in sensing the above analytes. The practical application for monitoring NZF/Fe3+ in water samples was also tested.