The effective joining between silicon nitride ceramics and metals is crucial for making full use of their excellent properties and meeting the service requirements of materials or components in complex environments. The gradient joining of silicon nitride ceramic (Si3N4) and molybdenum (Mo) with large physical properties difference was realized by a powder metallurgy gradient composite technology. The reaction mechanism of Si3N4 and Mo in each gradient layer under different sintering temperatures and Si3N4 additions was investigated. The transition layer structure of Si3N4/MoxSiy/Mo gradient material was optimized based on the reaction mechanism and the concentration distribution index p, obtaining the gradient connection of Si3N4 to Mo and improving the mechanical properties. The results show that Si3N4 and Mo mainly form molybdenum-silicon compounds through the diffusion reaction between Mo and Si. The reaction process follows (Mo+Si)→(Mo3Si/MoSi2+Si)→(Mo5Si3). The bending strength of Si3N4/MoxSiy/Mo gradient material reaches the maximum value of 371.42 MPa, the shear strength reaches the maximum value of 30.58 MPa, and the elements in the transition layer appear a quasi-continuous gradient distribution when p=1.5.