Electronic skin (e-skin), which mimics the tactile perception as human skin, is of interest to advance robotics, prosthetics, and human-machine interactions (HMI). However, the construction of artificial e-skin with the simulated function of morphology recognition and stimuli response remains challenging. Here, the design of a multifunctional and self-powered e-skin system based on the whisker-like magnetized micro-cilia array (MMCA) and the underneath flexible coils is reported. Owing to the excellent flexibility of the MMCA, the adaptive micro-cilia bending can be produced according to the tactile inputs or surface morphologies. With built-in magnetic moments, the MMCA deformation thus alters the magnetic flux distribution, which induces an electromotive force (voltage) in the coils for pressure detection and quantitative recognition of micro-scaled 3D morphologies. It is shown that using the distinct voltage intensities and waveforms, the optimized e-skin can be applied for real-time healthcare monitoring, Braille identification, and reconstruction of relief information. By customizing the magnetic moment alignments in MMCA, one e-skin device can further produce distinguishable signals to build up multi-commands for efficient HMI, e.g., underwater Morse code communication. Along with temperature tolerance and environmental immunity, the e-skin exhibits the potential to serve as an effective channel for intelligent 3D topology recognition and high-capacity communications.