1. Numerous evidence agree that global changes have altered plant phenology, abiotic factors and functional traits are center drivers linking phenology. However, few studies have considered the joint effects of these factors on flowering phenology under nitrogen (N) inputs and biodiversity loss. 2. A common garden experiment with two N addition and six plant diversity levels was established in Beijing. We assessed the effects of N addition and plant diversity loss on three flowering phenology events of Medicago sativa via functional traits and abiotic factors. 3. The first flowering day (FFD) delayed, the last flowering day (LFD) advanced, and flowering duration (FD) shortened after N addition. While FFD advanced, LFD delayed, and FD extended an average of 0.31, 0.64, and 0.95 days per species lost, respectively. Importantly, three analysis methods had been used to prove that the contributions of functional traits for the variance in flowering phenology changes was significantly larger than abiotic factors under biodiversity loss and N addition. 4. Our findings illustrate the non-negligible effects of functional traits on flowering phenology, and highlight the importance of including functional traits in phenology models to improve predictions of the response of plant phenology to N inputs and biodiversity loss.