Conservation tillage is an environmentally friendly and economical farming method, but its impact on rice yield is controversial. Artificially applied side deep fertilizing of machine-transplanted rice is when fertilizer is applied to the deep soil along with the machine transplantation of rice; this may improve the fertilizer utilization rate and rice yield and eliminate the possible negative effects of conservation tillage on rice yield. Using on machine-transplanted rice, this study aims to compare the effects of side deep fertilizing (SDF). We investigated the effects of artificially applying fertilizer (AAF) on rice growth and yield under conventional tillage (CT), reduced tillage (RT), and no tillage (NT). The rice root activity, root dry weight, leaf area index (LAI), net photosynthetic rate (Pn), chlorophyll content, panicle density, spikelets per panicle, and yield were all ranked as NT > RT > CT and SDF > AAF. The 1000-grain weight was also ranked as SDF > AAF. In addition, under NT conditions, the positive effect of SDF on rice growth and yield was higher than under RT and CT conditions. In general, conservation tillage combined with SDF saved costs and increased rice yield.