Respiration continues throughout the incubation of eggs and is closely related to fertilization status and changes in chick embryo growth. Here, we explored the relationship between egg respiration, fertilization status, and growth indicators during incubation. First, we studied the changes in respiration of eggs during incubation and found that O2 consumption and CO2 emission were increased gradually during incubation and reached a maximum value when the shells were broken by the chick (21 days). Next, we established models to classify eggs according to the difference in respiration between fertilized and unfertilized eggs early during incubation using random forest (RF), logical regression, and support vector machine (SVM). The accuracy rates of RF and SVM on the third day of incubation were 99.32% and 98.63%, respectively, and reached 100% on the fifth day. Finally, a linear model was used to establish the relationship between chicken embryo respiration and yolk free body mass (YFBM) (R2 values of 0.99 and 0.98 for the early and late incubation periods, respectively), heart mass (R2 = 0.94), liver mass (R2 = 0.97), and the digestive system (DS) mass (R2 = 0.98). The R2 values for the relationships between the real and the predicted YFBM values and heart, liver, and DS masses were 0.98, 0.89, 0.87 and 0.88, respectively, indicating the good fit of the model. This study provides a theoretical basis for the detection of sterile eggs and dead-embryo eggs during incubation.