For many applications envisioned for the Internet of Things (IoT), it is expected that the sensors will have very low costs and zero power, which can be satisfied by meta-material sensor based IoT, i.e., meta-IoT. As their constituent meta-materials can reflect wireless signals with environment-sensitive reflection coefficients, meta-IoT sensors can achieve simultaneous sensing and transmission without any active modulation. However, to maximize the sensing accuracy, the structures of meta-IoT sensors need to be optimized considering their joint influence on sensing and transmission, which is challenging due to the high computational complexity in evaluating the influence, especially given a large number of sensors. In this paper, we propose a joint sensing and transmission design method for meta-IoT systems with a large number of meta-IoT sensors, which can efficiently optimize the sensing accuracy of the system. Specifically, a computationally efficient received signal model is established to evaluate the joint influence of meta-material structure on sensing and transmission. Then, a sensing algorithm based on deep unsupervised learning is designed to obtain accurate sensing results in a robust manner. Experiments with a prototype verify that the system has a higher sensitivity and a longer transmission range compared to existing designs, and can sense environmental anomalies correctly within 2 meters.