The establishment of a standard growth model for the whole crop life cycle is necessary to guide the acquisition of the best crop “prescription” (accurate decision-making and execution of operations). The intelligent identification technology of crop fertility stages is one of the important technologies to build the standard crop growth model. Under the situation of large-scale crop cultivation in Hulun Buir Dahewan, the traditional method of collecting and identifying crop fertility phenotype data based on manual experience or a single sensor will lead to problems such as limited collection range and low identification efficiency. In order to address the above problems, a series of optimizations are proposed for the overall system. First, in the data collection stage, a complete “air-ground-human” integrated crop phenotype data collection system is proposed in this study. In addition, in the data analysis stage, an improved intelligent identification system of crop fertility stages is proposed based on different crop phenotype data. The proposed identification system can provide real-time and accurate information about the current crop fertility stages, which serves as an excellent basis for establishing a standard growth model for the whole crop life cycle.