Seed enterprises are crucial for ensuring national food security, the driving force behind the seed industry’s advancement, and the core entity in constructing a modern seed industry system. At the micro and macro levels, agricultural seed enterprises face challenges and pressures in earning excess profits, enhancing their competitive edge, and resisting the incursion of multinational seed enterprises. This article selects panel data from 49 listed seed enterprises in China from 2015 to 2022 and uses methods such as global principal component analysis (GPCA) and Q-type cluster analysis to measure and evaluate the competitiveness of Chinese seed enterprises. Research has found that: (1) From 2015 to 2022, the overall competitiveness of listed Chinese agricultural seed enterprises has shown an upward trend. The competitiveness of agricultural seed enterprises can be further decomposed into operational capabilities, growth capabilities, production efficiency, technological innovation capabilities, etc. (2) The top ten agricultural seed enterprises in China have obvious advantages in operational and technological innovation capabilities, but their growth capabilities and production efficiency are insufficient. (3) Regarding the vertical comparison of the seed industry, the ranking of the competitiveness of Chinese listed agricultural seed enterprises from strong to weak is wheat seed enterprises > other seed enterprises > melon and vegetable seed enterprises > corn seed enterprises > rice seed enterprises. (4) Compared with international seed industry giants, there are various reasons why China’s top agricultural seed enterprises have weaker competitiveness, specifically reflected in research and development investment, scale and market share, industrial layout, and other aspects. The findings of this research offer empirical evidence to bolster the competitiveness of seed enterprises and advance the seed industry, while also aiding in fortifying the nation’s strategic oversight of the seed sector, bearing profound implications for safeguarding food security.