Elevated temperature, elevated CO2 concentration, and their combination significantly promoted the number and biomass of female mulberry (Morus alba L.) flowers, but the opposite is true for males. This paper demonstrates that male mulberry trees would suffer more negative effects on floral development and differentiation under global warming. With the ongoing intensification of global warming, flower formation has attracted widespread interest because it is particularly vulnerable to the effects of environmental factors. However, current knowledge of floral development regarding gender and sex differentiation under elevated temperature, CO2 concentration, and their combination remains limited. The aims of this study were to assess how sex-related differences in the morphology, biomass, and carbon (C) and nitrogen (N) contents of flowers respond to elevated temperature and CO2 concentration. Morus alba L. saplings (monoecious plants) were subjected to two temperature conditions (ambient vs. ambient + 2 °C) and two CO2 regimes (ambient vs. ambient + 380 ppm CO2) in growth chambers for 18 months growth, and differences in flowering phase, sex ratio, floral morphology and biomass, as well as total carbon and nitrogen of male and female inflorescences were investigated. Elevated temperature, elevated CO2 concentration, and their combination significantly increased the number and biomass of female inflorescences but decreased the number and biomass of male inflorescences. Furthermore, the combination of elevated temperature and CO2 concentration significantly decreased ovary length and C/N ratio of female flowers and the fresh weight of male flowers. Additionally, C/N ratio was negatively related to morphological traits of male inflorescences but positively related to tepal length of female flowers. These findings indicate that global warming may affect floral development and sex differentiation in mulberry and that the male inflorescences of M. alba may suffer more negative effects than female inflorescences with respect to flower number, biomass, and morphological development.