Secondary electron emission (SEE) of solid materials due to electron bombardment is influenced by numerous properties of materials, where the surface condition plays a critical role in the value of secondary electron yield (SEY). Here, a 3D random microstructure surface model is established to simulate realistic surface morphology and study its effects on SEY by implementing a path tracing algorithm and finite element method. It is found that electron collision frequency on surfaces is strongly affected by local surface geometry parameters, namely the vertical height and the distance between similar features along the horizontal direction of random microstructure surfaces. Manipulating the interaction angle and the inter-barrier collision frequency could quantitively suppress or intensify SEE, allowing for functional design of solid material surfaces under various contexts. In addition, empirical roughness parameters (Ra, Rz) lack certain microscopic information. A method is proposed to estimate secondary electron yield numerically for a given material surface geometry. It provides copious utilities in practical SEE-related applications.