The primary oil layer of the Yanchang East Oilfield are situated with an average depth of 670 meters and possess an average permeability of 0.3~0.5 mD. This marks it as an ultra-low permeability shallow oil reservoir. Horizontal fractures are easily formed during oil well fracturing, resulting in rapid water flooding when water injection development is conducted. This results in a significant decrease in oil well production and low recovery rate. To address this challenge, a bottom water injection development method is proposed based on the study of the characteristics of horizontal fracture water injection seepage, the water flooding pattern of fractured horizontal fracture oil wells, and the mechanism of bottom water injection. Three parameters, specifically permeability variation coefficient, breakthrough coefficient, and grade difference, are applied to comprehensively characterize the characteristics of water breakthrough and non-water breakthrough layers, thereby providing a basis for bottom water injection layer selection. Indoor nuclear magnetic resonance online testing and core flow displacement experiments are conducted in conjunction with reservoir numerical simulation and on-site tracer testing to optimize the water injection parameters. The individual well oil production of the three well groups conducting bottom water injection pilot tests rose from 0.054 t/d to 0.179 t/d. The water content decreased from 15% to 10%, the formation pressure grew by 0.18 MPa, and the predicted final recovery rate escalated by 2.1 percentage points, delivering impressive results. Research has shown that the water injection development effect is optimal when the coefficient of variation of permeability is less than 0.5, the breakthrough coefficient is less than 1.5, the permeability level difference is less than 5, the injection rate is 0.06 mL/min, and the injection pressure is 7 MPa. Bottom water injection can effectively solve the issue of poor water injection development effect in shallow horizontal fracture reservoirs, providing reference for efficient water injection development in reservoirs of the same nature.