Lead-zinc flotation wastewater discharge poses a growing risk to environmental safety, and efficient treatment is challenging due to large quantities of water, combined pollution, and the limitations of current approaches. This study discussed the removal differences, available treatment approach, interaction characteristics, and mechanisms of heavy metals (Pb2+ and Zn2+), flotation reagents (butyl xanthate (BX), and dianilino dithiophosphoric acid (DDA)) in single and composite systems using electrocatalytic internal micro-electrolysis (ECIME). Density functional theory (DFT), solubility, and UV spectrum analyses revealed that the high chemical potential of the (BX)2M, (DDA)2M complexes in lead-zinc flotation wastewater played key roles for the solubility and ECIME removal of these pollutants. The complexes significantly inhibited activated carbon (AC) interface adsorption, as well as DDA and (DDA)2M degradation and Fe(II)–Fe(III)–OH flocculation. Prolonging the treatment times for Pb2+, Zn2+, BX, and (BX)2M effectively alleviated the inhibitory effect. However, cyclic voltammetry (CV) and X-ray photoelectron spectroscopy (XPS) analysis also highlighted the difficulty of the electrochemical reduction deposition of the Pb2+ and Zn2+ reactions. Comparatively, the DDA and (DDA)2M in composite systems showed higher electrochemical stability, while degradation was highly dependent on high voltage and exhibited temporal hysteresis in the ECIME system. The DDA removal rate only reached 60% after ECIME treatment at 45 V for 90 min, while the values of Pb2+ and Zn2+ (9 V, 30 min) and BX (18 V, 70 min) exceeded 90% and exhibited significantly disadvantage effect when voltage was larger than 18 V. Based on the their distinguishing characteristics of ECIME removal and flotation beneficiation effect, an alternative suggested removing of Pb2+, Zn2+ and BX while preserving DDA and (DDA)2Pb in lead-zinc flotation wastewater could be achieved by regulating the reaction potential and time. By adjusting the ECIME settings to a voltage of 15.2 V, a period of 45 min, and a pH of 5.5, a comprehensive removal rate of 97.59% was achieved. Additionally, recycling wastewater at proportions of 50–70% will not lead to confusion in the selection of lead-zinc ore. The results demonstrated the feasibility and economic efficiency of selective removal and reuse, showing considerable potential for practical application.