Background: Low-temperature stress significantly restricts maize germination, seedling growth and development, and yield formation. However, traditional methods of evaluating maize seedling quality are inefficient. This study established a method of grading maize seedling quality based on phenotypic extraction and deep learning. Methods: A pot experiment was conducted using different low-temperature combinations and treatment durations at six different stages between the sowing and seedling phases. Changes in 27 seedling quality indices, including plant morphology and photosynthetic performance, were investigated 35 d after sowing and seedling quality grades were classified based on maize yield at maturity. The 27 quality indices were extracted, and a total of 3623 sample datasets were obtained and grouped into training and test sets in a 3:1 ratio. A convolutional neural network-based grading method was constructed using a deep learning model. Results: The model achieved an average precision of 98.575%, with a recall and F1-Score of 98.7% and 98.625%, respectively. Compared with the traditional partial least squares and back propagation neural network, the model improved recognition accuracy by 8.1% and 4.19%, respectively. Conclusions: This study provided an accurate grading of maize seedling quality as a reference basis for the standardized production management of maize in cold regions.