The invention relates to a microgrid multi-energy joint optimal scheduling method. The method includes: step 1, on the basis of force application conditions of energy supply equipment and operating states of energy storage equipment in different scenes, constructing a physical model of a multi-energy system; step 2, establishing unit mathematical models, including a wind power generator model, a photovoltaic power generation model, a micro-gas turbine model, a fuel cell model and an energy storage model, of the microgrid multi-energy system; step 3, in order to realize lowest comprehensive cost in system operation, constructing a microgrid multi-energy optimal scheduling model by taking DG operation constraints, system safety constraints and multi-energy coupling characteristics into comprehensive consideration; step 4, on the basis of reversed order dynamic planning, solving the microgrid multi-energy optimal scheduling model to obtain a microgrid multi-energy joint optimal operatingstrategy. By the microgrid multi-energy joint optimal scheduling method, operating demands in different scenes can be met, electricity-thermal coordinated optimal scheduling schemes are provided for operating of a comprehensive energy microgrid in different scenes, and high integral operating efficiency and high economic benefits are realized.