In order to explore the effects of different fertilization frequencies on soil water and nutrient transport and tomato yield under the condition of alternate partial root-zone drip irrigation (ADF), and seek for efficient water and fertilizer regulation measures in tomato production. The experiment set three irrigation and fertilization frequency treatments F3 (3 d), F6 (6 d), F12 (12 d) under ADF and a conventional drip irrigation fertilization treatment as control (CK, frequency is 6 d). The results showed that in 0-40 cm soil layer, the two years average soil water content and inorganic nitrogen content of high-frequency irrigation and fertilization treatment (F3) were increased by 7.9% and 28.3% compared with low-frequency treatment (F12) during the growth period. In the 40-60 cm soil layer, the two years average accumulation amount of inorganic nitrogen of F3 and F6 treatment decreased by 37.8% and 23.0%, respectively, compared with that of F12 treatment. Compared with F12 treatment, the average tomato biomass, nitrogen uptake and yield of F6 treatment in two years increased by 16.8%, 15.2% and 22.6%, respectively, but there was no significant difference between F6 and F3 treatment. Under the same fertilization amount and irrigation fertilization frequency, F6 treatment reduced 40% of the irrigation amount while maintaining the same yield as CK. Therefore, appropriately increasing the frequency of irrigation and fertilization can promote tomato growth and yield formation, and ADF has greater water-saving and stable yield effect than conventional drip irrigation and fertilization. This study recommended that applying fertilizer once every 6 days under ADF could be a more efficient water and fertilizer management measure in greenhouse tomato production.