With the gradual improvement of people’s health awareness, wearable devices occupy an important position in daily health care and human physiological activity monitoring. As traditional silicon-based electronic products face problems such as interface mismatch, silk fibroin has gradually become an alternative choice for next-generation wearable electronic devices due to its excellent performance. Herein, an ultra-thin transparent and flexible multi-functional sensor based on silk hydrogel with self-patterned microstructure is proposed. The silk hydrogel exhibits superior transparency (>82%) and thin thickness (∼100 μm). Furthermore, the self-patterned microstructure on the silk hydrogel surface is beneficial for the high sensitivity of pressure sensing response (1.6 kPa−1). This device exhibits advantageous performance on temperature (top sensitivity of 6.25% °C−1) and humidity (top sensitivity of 0.16% RH−1) sensing response. It also shows fast response (0.16 s) and durable stability (over 2000 dynamic cycles). Moreover, this device can be applied to monitor human facial expression, joint movements, temperature change, breathing and other health indicators. It is worth mentioning that this multi-functional sensor can monitor the signal of breathing and throat, so it can be applied to the clinical physiological activity monitoring of patients with upper respiratory tract infection. In addition, we also demonstrate a grasping and relaxing experiment of intelligent manipulator to verify the pressure and temperature sensing performance, providing a possibility for its application in the field of prosthetics. According to these advantages, the reported ultra-thin transparent multi-functional sensor based on silk hydrogel has broad prospects in the fields of health monitoring, intelligent prosthetics, and electronic skin, etc.