Nitrogen deposition and biodiversity alter plant flowering phenology through abiotic factors and functional traits. However, few studies have considered their combined effects on flowering phenology. A common garden experiment with two nitrogen addition levels (0 and 6 g N m−2year−1) and five species richness levels (1, 2, 4, 6, and 8) was established. We assessed the effects of nitrogen addition and plant species richness on three flowering phenological events ofMedicago sativaL. via changes in functional traits, soil nutrients, and soil moisture and temperature. The first flowering day was delayed, the last flowering day advanced, and the flowering duration shortened after nitrogen addition. Meanwhile, the last flowering day advanced, and flowering duration shortened along plant species richness gradients, with an average of 0.64 and 0.95 days change per plant species increase, respectively. Importantly, it was observed that plant species richness affected flowering phenology mainly through changes in plant nutrient acquisition traits (i.e., leaf nitrogen and carbon/nitrogen ratio). Our findings illustrate the non-negligible effects of intraspecific variation in functional traits on flowering phenology and highlight the importance of including functional traits in phenological models to improve predictions of plant phenology in response to nitrogen deposition and biodiversity loss.