Climate warming is changing above-ground phenology of plants around the world1, 2. However, warming effects on below-ground phenology of plants are unclear despite that roots play a vital role in carbon cycling3. By conducting a global meta-analysis, we show a phenological mismatch between above- and below-ground plant responses to climate warming. Herbaceous plants advanced both the start and end of the growing season based on their above-ground responses, resulting into a shorter growing season. Below-ground phenophases did not exhibit any obvious changes in herbaceous plants. In contrast, climate warming did not affect the length of above-ground growing season but extended the below-ground growing season of woody plants. These results highlight that climate warming can differentially affect above- and below-ground plant phenology with mismatches arising in herbaceous plants via less responsive below-ground phenology whereas mismatches in woody plants via more responsive below-ground phenology. Mismatches in above- and below-ground plant phenology imply that terrestrial carbon cycling models exclusively based on above-ground responses are less accurate, which highlight the urgent need to incorporate below-ground plant phenology into future Earth system models.