To explore fertilization strategies that achieve both high yield and emission reduction in greenhouse tomato production, a two-season experiment was conducted in autumn 2023 and spring 2024 under equal nitrogen input. Seven treatments were established: conventional fertilization (CK1), biogas slurry alone (CK2), 0.5% biochar + biogas slurry (T1), 2% biochar + biogas slurry (T2), dicyandiamide + biogas slurry (T3), 0.5% biochar + biogas slurry + dicyandiamide (T4), and 2% biochar + biogas slurry + dicyandiamide (T5). The effects of each treatment on tomato root traits, yield, irrigation water use efficiency (IWUE), partial factor productivity of nitrogen (PFPN), and soil N₂O emissions were systematically evaluated. An analytic hierarchy process (AHP) was applied for comprehensive assessment. The results showed that fertilization treatments significantly affected tomato root traits (p < 0.05), with T5 exhibiting the best performance in root length, average diameter, total surface area, total volume, and root activity, all significantly higher than CK1. T5 also achieved the highest yield in both seasons, with increases of 8.13% (autumn 2023) and 10.19% (spring 2024) over CK1. Moreover, T5 showed superior IWUE (475.38 kg ha⁻¹ mm⁻¹) and PFPN (405.92 kg kg⁻¹). In terms of environmental performance, T5 significantly reduced soil N₂O flux, with the largest reduction reaching 16.16%, particularly during the peak emission stages in the flowering and fruit-setting periods. The AHP-based comprehensive evaluation confirmed that T5 had the highest overall weight with satisfactory matrix consistency. In conclusion, compared with conventional fertilization, the integrated T5 treatment increased tomato yield by up to 10.19% and reduced cumulative N₂O emissions by up to 16.16%, highlighting its potential as a feasible fertilization pathway and technical reference for low-carbon and sustainable agriculture.