Flocculation is an economical and effective pretreatment technology for landfill leachate. An iron salt flocculant is often used in landfill leachate pretreatment, but the flocs that are formed are affected by the operation sequence, which subsquently influences flocculation. This study selected three representative landfill leachates (i.e., mature landfill leachate (MLL), biologically treated landfill leachate (BTL), and nanofiltration concentrate leachate (NFCL)). The effect of different operation modes on the removal of organic matter from landfill leachate by flocculation was studied, and a strategy to control colloidal instability is put forward. The results revealed that adjusting the pH value to 9 using NaOH changes the zeta potential of leachate when the leachate and sludge are not separated, which affects electric neutralization in flocculation and colloidal stability. Furthermore, a part of the collected organic matter is released to the leachate again, leading to a decrease in the flocculation pretreatment effect. In this improved flocculation process, the leachate and sludge are first separated, and the pH value of the system is then adjusted to 9. The effect of OH− on electric neutralization is avoided and the remaining Fe3+ can further remove organic matter from leachates. Finally, the UV254 removal efficiencies of MLL, BTL, and NFCL increased by 20.38%, 28.67%, and 22.67%, respectively. In a full-scale application, i.e., an NFCL treatment facility, the UV254 removal efficiency during long-term operation reached 87.50%. Therefore, the colloid instability control strategy this study proposes can provide theoretical and engineering references for the flocculation pretreatment of landfill leachate.