Recently, a novel controlled-release N fertiliser (CRNF) application method using basal CRNF combined with urea top-dressing at the tillering stage has been proposed to enhance rice yield and N use efficiency (NUE). However, its effect on ammonia volatilisation (AV) loss and the yield and NUE of blanket-seedling machine-transplanted rice are unknown. A field experiment was performed to investigate the effect of three types of CRNF (slow-release blending fertiliser (BSRB), polymer-coated urea (PCU) and sulphur-coated urea (SCU)) and two fertilisation regimes (a single basal application (B) and a basal CRNF application combined with urea top-dressing at the tillering stage (BT)) on grain yield, NUE and AV loss from paddy soil of blanket-seedling machine-transplanted rice. Conventional high-yield fertilisation (four split applications of urea at 270kgNha−1 (CK)) and 0-N treatments were established as controls. The results demonstrated that the AV flux values from paddy soil varied in distinct patterns for the different CRNF treatments. The cumulative AV loss in the urea treatment during the basal (the first week) and tillering fertiliser (the second week) comprised the majority of the total AV loss, both accounting for 87.2% in each year. Compared with CK, B-BSRB significantly reduced AV loss during the first two weeks and the total AV loss by 24.7% and 27.9% in 2013 and 2014, respectively. B-SCU and B-PCU generally showed no benefits for reducing AV loss relative to urea. Compared with B-PCU and B-SCU, B-BSRB met the N demand of rice, substantially mitigated N loss via AV in paddy fields, and improved yield and NUE of Blanket-seedling Machine-Transplanted rice. The effect of BT for each CRNF on AV loss was not consistent. The BT-BSRB and the BT-SCU correspondingly mitigated AV loss to a certain extent in each year, mostly due to the relatively lower AV loss during the first week, and no significant increase in AV loss at the second week. The BT-BSRB incurred not only the lowest AV loss of 39.7kgNha−1 and 37.8kgNha−1 but also the highest yield of 11.6tha−1 and 10.1tha−1 and an NRF of 48.8% and 52.4% in 2013 and 2014, respectively. Our results suggested that combining BSRB and BT optimised rice yield and nitrogen use efficiency while decreasing ammonia volatilization from paddy soil of blanket-seedling machine-transplanted rice.