No-tillage with residue coverage has been proven for protection of agricultural soils worldwide. However, in Northeast China, inconsistent maize yields under no-tillage system have hindered the broad adoption of this practice and its mechanisms in yield reduction remain unclear. This study therefore aimed to determine key factors affecting growth and yield of maize under no-tillage with residue coverage in the semi-humid region of Northeast China. The experiment included conventional tillage (CT), no-tillage with 100% residue coverage (RC), and no-tillage with 30% residue removal (RR) in maize fields in Jilin, Northeast China. From 2017 to 2019, we measured soil physical and chemical properties, phenological period (PP), dry matter accumulation (DMA), and maize yield in field experiments. The results showed that the RC and RR treatments increased soil organic C and nutrients in the 0–5 cm soil layer, and soil water content in 0–30 cm soil layers, compared with the CT treatment. However, residue coverage, especially in the RC treatment, decreased soil temperature during the early stages of maize growth and delayed the time of emergence and PP and decreased DMA and yield in maize. The maize yield of the RC treatment was 10.35% less than that of CT, whereas there was no difference between the RR and the CT treatments. Structural equation modeling (SEM) demonstrated that the reduction in soil temperature from the time of sowing to emergence under no-tillage is a primary reason for the observed reduction in maize yield. Our results indicate that no-tillage systems with partial residue cover may maintain maize yield and protect black soils in the semi-humid region of Northeast China.