Single-time fertilization (STF) of controlled release blended fertilizer (CRBF) improves grain yield and nitrogen use efficiency (NUE) in rice production.  However, the impact of soil nitrogen (N) distribution and root growth on rice yield and NUE under STF of CRBF remains unclear.  This two-year field experiment investigated the effects of fertilizer types (normal urea (U) and CRBF) and single-time fertilization methods (broadcast and side-deep fertilization) on the soil N distribution, plant N uptake, root characteristics, grain yield and NUE.  The results showed that CRBF under STF averaged increased plant dry matter accumulation, N uptake, grain yield, nitrogen recovery efficiency (NRE), and nitrogen agronomic efficiency (NAE) by 8.29, 21.85, 10.57, 79.28, and 74.8% compared to the other treatments, respectively.  Side-deep fertilization of CRBF further increased NUE by 12.78% compared to broadcast.  Moreover, CRBF under STF increased leaf SPAD value and glutamine synthetase (GS) /glutamine oxoglutarate aminotransferase (GOGAT) activity by 5.93 and 25.58%.  CRBF under STF increased the soil inorganic N concentration and showed a “rising early and stabilizing later” characteristic.  Additionally, CRBF under STF improved rice root growth and averaged increased root biomass, total root number, root average diameter, total root length, total root surface area, total root volume by 28.30, 28.56, 18.64, 13.38, 35.26, and 37.06% at tillering and heading stages, respectively.  Partial least squares path modeling indicated that CRBF under STF increased soil inorganic N concentration to improve root morphology, thereby increasing N uptake and improving and rice yield and NUE.  Taken together, our findings support that CRBF with single-time fertilization is the preferred N fertilizer strategy for achieving high yield and efficiency in rice and that side-deep fertilization is the optimal fertilization method.