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In this paper, an auxiliary equation method is introduced for seeking exact solutions expressed in variable coefficient function forms for fractional partial differential equations, where the concerned fractional derivative is defined by the conformable fractional derivative. By the use of certain fractional transformation, the fractional derivative in the equations can be converted into integer order case with respect to a new variable. As for applications, we apply this method to the time fractional two-dimensional Boussinesq equation and the space-time fractional (2+1)-dimensional breaking soliton equation. As a result, some exact solutions including variable coefficient function solutions as well as solitary wave solutions for the two equations are found.