Kesterite Cu₂ZnSn(S,Se)₄ (CZTSSe) presents a promising low-cost and sustainable photovoltaic material. However, its performance is critically hindered by uncontrollable complex crystallization during high-temperature selenization and the detrimental formation of a MoSe₂ back contact layer, which induces significant carrier recombination losses, imposing severe limitations on open-circuit voltage (V_OC) and fill factor (FF). Addressing the challenge of achieving high-quality CZTSSe absorbers and interfaces, this study introduces a novel thermal modulation strategy during selenization. By optimizing nucleation and crystallization through a controlled slow heating stage—distinct from conventional sustained high-temperature processes—this method yields more uniform CZTSSe grains, effectively suppresses runaway growth of the interfacial MoSe₂ layer, and inhibits absorber decomposition at the interface. Consequently, interface defect density is substantially reduced, leading to enhanced carrier transport properties. Devices fabricated using this method within the Cu²⁺–Sn²⁺–N,N-dimethylformamide (DMF) precursor system achieved a significant power conversion efficiency (PCE) increase from 8.02% to 11.65%, driven by a V_OC rise from 409 to 489 mV and a substantial FF enhancement from 54.34% to 63.63%. Furthermore, the method demonstrates excellent process compatibility, achieving PCEs of 13.72% and 13.81% in Cu⁺–Sn⁴⁺–DMF and Cu⁺–Sn⁴⁺–methoxyethanol (MOE) systems, respectively. This work underscores the crucial importance of the CZTSSe/Mo interface and provides new insights and pathways for fabricating high-quality absorbers and efficient kesterite solar cells.