Soil drought, uneven distribution of precipitation, low precipitation use efficiency and excessive chemical fertilizer input are critical factors limiting sustainable agriculture of rainfed apple orchards in the Loess Plateau, China. For alleviating the effects of these factors and improving yield of rainfed apple orchards in this region, we proposed partial organic fertilizer replacement (substitution rate: 60% total nitrogen from organic fertilizer and 40% total nitrogen from chemical fertilizer) combined with rainwater collection (ORRC) system and conducted an in-situ field experiment for three years (2016–2018) with significant interannual precipitation variation to investigate the effects of ORRC system on soil water content (SWC), soil water storage (SWS), soil desiccation index (SDI), soil water storage deficit degree (SWSDD), nitrate-nitrogen, apple yield, crop water productivity (CWP) and precipitation use efficiency (PUE) in different rainfall years. Three management methods: (1) partial replacement of chemical fertilizer by organic fertilizer combined with rainwater collection measure (ORRC), (2) rainwater collection measure only (RC), and (3) conventional measure without any rainwater collection measure (CK). The results indicated that compared with CK treatment, ORRC treatment significantly (P < 0.05) increased SWC in 0–280 cm soil depth at spring and autumn by 26.91% and 32.19% in three years, respectively, alleviating heavy spring drought in rainfed apple orchards. Compared with RC and CK treatments, ORRC treatment had 37.89% and 52.49% lower soil water storage deficit degree (SWSDD) and 25.97% and 69.74% higher soil desiccation index of 0–280 cm depth, and improved nitrate-nitrogen content of 0–200 cm depth by 12.03 and 12.75 mg kg⁻¹ in three years, respectively. ORRC and RC treatments improved apple yield by 47.40% and 11.43%, CWP by 55.45% and 19.66% and PUE by 46.50% and 11.69% over three years in comparison with CK treatment, respectively. In particular, ORRC treatment had the highest apple yield, CWP and PUE in each year. Overall, partial organic fertilizer replacement combined with rainwater collection measure holds promise for improving apple orchard production of rainfed apple orchards in northern Shaanxi of China.