Carbon dioxide (CO2) is always maintained at ambient levels by ventilation in commercial egg incubators. However, elevated CO2 levels during the early and late periods have been reported to improve the quality of chicks and shorten the hatch window. This study investigated the effect of precise CO2 supplementation during the early and late periods of incubation on embryo growth and incubation performance by developing and using a CO2 supplementation system to increase the CO2 level in an experimental egg incubator. The CO2 level was maintained at 1% in the early period (from the beginning to the 10th day of incubation, E0-E10) and in the late period (from internal pipping (IP) to the 21st day of incubation (E21), IP-E21) in an incubator for the treatment group, whereas the CO2 level was maintained at the ambient level in the other incubators for the control group. A comparative assessment of embryonic development, hatching characteristics, and hormone and nutrient levels was conducted for each trial. The experiment comprised three trials, with 300 Jing Hong No. 1 breeding eggs in each incubator. The elevated CO2 treatment significantly shortened the chick hatching time (H0) by 4 h (P < 0.05) and the hatch window by 3 h (P < 0.05) without affecting hatchability, chick weight at 1 d of age, brooding period, or quality score. At external pipping (EP), the heart weight, intestinal weight, relative intestinal weight, and relative heart weight in the treatment group were significantly higher than those in the control group (P < 0.05). In addition, the embryonic intestine, relative intestine, and relative heart weights of the newly hatched chicks in the treatment group were significantly higher than those in the control group (P < 0.05) at H0. The treatment significantly increased the concentration of corticosterone in the embryonic plasma during the period from IP to EP (P < 0.05), promoted the secretion of triiodothyronine and tetraiodothyronine (P < 0.05), and increased the glycogen content of the embryonic liver on E21 (P < 0.05). This result indicates that elevated CO2 (1%) during the early and late periods of incubation accelerated embryonic organ development and shortened the chick hatching time and hatch window without affecting hatchability or hatchling quality, which can be explained by the synergistic functions of the secretion of plasma corticosterone and thyroid hormones and the accumulation of liver glycogen between the early and late periods of incubation.