Effective root-shoot coordination optimizes root development, enhances photosynthesis, and ultimately increases crop yield. Aerated drip irrigation (AI) and nitrogen application are widely recognized for their roles in improving crop productivity. However, the mechanisms through which these practices influence root-shoot coordination to modulate tomato yield remain unclear. Therefore, a two-year greenhouse experiment was conducted to investigate the effects of irrigation method and nitrogen application rate on tomato root growth and distribution, photosynthetic performance, biomass accumulation and distribution, root-to-shoot ratio (R/S), and apply the Mantel test to analyze the effects of indicators on tomato yield. Treatments included two drip irrigation methods (AI: aerated drip irrigation, CK: conventional drip irrigation) and five nitrogen levels (0, 50, 150, 200, and 250 kg N ha(-1); N1-N5). The results indicated that AI and nitrogen application significantly enhanced root activity (P < 0.05), promoted the fine root formation (<1 mm diameter), and increased deep root distribution (>20 cm). AI also positively regulated photosynthetic performance, which increased with nitrogen rate up to N4 before declining. At maturity, the AIN4 treatment increased leaf area index (LAI), chlorophyll content (SPAD), and net photosynthetic rate (P-n) by 14.11 %, 26.53 %, and 18.68 %, respectively, compared with other treatments. It also enhanced dry matter accumulation in stems, leaves, and fruits and promoted assimilate transport to fruits. Tomato yields under AIN4 reached 109.00 t ha(-1) and 103.09 t ha(-1) over two years, which were 4.68-5.06 % higher than those under CKN5, while also reducing nitrogen application by 20 %. The effect of AI on R/S varied seasonally, decreasing during spring-summer cultivation and increasing during autumn-winter cultivation. Maximum R/S, root surface area-to-LAI (RSA/LAI), and fine root length-to-LAI (FRL/LAI) occurred under N4. These results indicate that AIN4 optimizes root-shoot coordination, promotes balanced biomass accumulation, and ultimately maximizes yield, suggesting its suitability for greenhouse tomato cultivation in arid Northwest China.