Microstructures with stimulus-responsive deformation capabilities can convert external stimulation signals to generate mechanical deformation, holding significant potential for frontier applications in automation technology, micro-robotics, and microfluidic chips. However, the development of intelligent microstructures relies on smart materials and shaping technologies, which are not only limited to a few material systems but also confined to single-stimulus responsive deformation. This work proposes a novel approach to fabricate protein microstructure arrays on shape-memory thin films using femtosecond laser two-photon additive manufacturing technology, achieving dual-responsive deformation of microstructure array size and period. Initially, the microstructure array is mechanically stretched and characterized under heat treatment, enabling control of the structural period, which can be restored under thermal stimulation. Simultaneously, bovine serum albumin microstructures exhibit reversible swelling and contraction deformation under different pH conditions. Combining smart materials with shape-memory substrates imparts more complex and controllable dual-responsive deformation to the microstructure array. This study offers beneficial exploration for the application of intelligent microstructure arrays in microfluidic systems.