Yield loss of ratoon crops caused by the rolling damage to the left stubble from mechanically harvesting main crops has been reported in previous studies. However, limited attention has been paid to identify the effect of the mechanical harvesting of the main crop on the yield of a non-rolled zone (NRZ) of a ratoon crop. A two-year field experiment on ratoon rice with two harvest methods (mechanical harvesting: MEH; manual harvesting: MAH) of a main crop was conducted to identify whether there is a border effect on the yield of the NRZ, and to evaluate whether the border effect will compensate for the yield loss of the ratoon crop. On average, MEH reduced the grain yield of the ratoon crop by 17.6% compared with MAH. The yield of the rolled zone (RZ) in MEH was 66.1–70.3% lower than that of MAH, which was attributed to the lower panicle m−2, grain filling percentage, total dry weight, and harvest index. In contrast, the yield of the NRZ in MEH was 2.7–10.8% higher than that of MAH. The yield differences of the non-rolled single row (R1), side row (R2), and middle row (R3) in the NRZ compared with MAH were 22.9%, 8.5%, and −10.1%, respectively, which were mainly explained by the panicle m−2, spikelets m−2, total dry weight, and regeneration rate. These results suggest that rolling during the mechanical harvesting of the main crop induced a border effect on the yield of the NRZ, which reduced the yield loss of the ratoon crop. The yield gain of the NRZ was attributed to the increased yield of R1 and R2 rather than R3.