Highly programmable shape morphing of 4D-printed micro/nanostructures is urgently desired for applications in robotics and intelligent systems. However, due to the lack of autonomous holistic strategies throughout the target shape input, optimal material distribution generation, and fabrication program output, 4D nanoprinting that permits arbitrary shape morphing remains a challenging task for manual design. In this study, we report an autonomous inverse encoding strategy to decipher the genetic code for material property distributions that can guide the encoded modeling toward arbitrarily pre-programmed 4D shape morphing. By tuning the laser power of each voxel at the nanoscale, the genetic code can be spatially programmed and controllable shape morphing can be realized through the inverse encoding process. Using this strategy, the 4D-printed structures can be designed and accurately shift to the target morphing of arbitrarily hand-drawn lines under stimulation. Furthermore, as a proof-of-concept, a flexible fiber micromanipulator that can approach the target region through pre-programmed shape morphing is autonomously inversely encoded according to the localized spatial environment. This strategy may contribute to the modeling and arbitrary shape morphing of micro/nanostructures fabricated via 4D nanoprinting, leading to cutting-edge applications in micro fluidics, micro-robotics, minimally invasive robotic surgery, and tissue engineering.