Aggregating metadata in the ciphertext field is an attractive property brought by homomorphic encryption (HE) for privacy-sensitive computing tasks, therefore, research on the next-generation wireless networks has treated it as one of the promising cryptographic techniques for various scenarios. However, existing schemes are far from being deployed in various computing scenarios due to their high computational complexity and ciphertext expansion, especially for bandwidth-limited and latency-sensitive wireless scenarios. In this paper, we propose the AirHE scheme to achieve homomorphic evaluation via the over-the-air computation in the physical layer. Moreover, we propose a new encryption scheme that can be integrated with the physical layer procedure. A new error control mechanism for ciphertext is further proposed to solve the error accumulation problem. The novelty of the AirHE scheme is to take advantage of the intrinsic superposition characteristic of the wireless channel, such that the communication and computation cost is greatly reduced by achieving homomorphic evaluation and error control of ciphertext in the physical layer. We implement the AirHE scheme based on the LTE system and validate its feasibility. Simulation results are also presented to show the performance of the AirHE scheme under different channel conditions.