As an eco-friendly vineyard floor management, mulching can effectively control weeds, preserve soil moisture, reduce irrigation requirements, and modify the grapevine microclimate. However, its impact on the grapevine microclimate, as well as the variation in grape and wine flavonoids across different growth stages under mulching conditions remains insufficiently studied. Therefore, in the vineyard of a semi-arid region, the whole-field mulching (M) of black geotextile mulch was applied to Vitis vinifera Marselan grapevines from anthesis and removed at three phenological stages. The grape and wine flavonoids during the growing season were evaluated through HPLC-MS, and the transcriptomic data was analyzed in three vintages (2015-2017). Results showed that mulching weakened over 30°% of reflected light, and especially light with longer wavelengths. Mulching helped to reduce water evaporation and lead to higher soil water content. As for berry composition, M slightly decreased the berry weight and accelerated sugar accumulation when mulch removal. Controlled grapes presented higher flavonols at harvest while mulch removal around veraison enhanced the accumulation of anthocyanins. The reflected photosynthetic active radiation, cluster temperature, and soil moisture played important roles in flavonoid regulation. Key genes including VviFLS1, VviLAR1, and VviANR, as well as MYB transcription factors MYBF1, MYBA1, and MYB3 are responsible for flavonoid regulation. M slightly affected the wine flavor profile but improved the wine's appearance. In conclusion, M effectively suppresses weed growth and modifies grapevine microclimate in semi-arid climates, mulch removal around veraison favored the accumulation of grape flavonoids.