This paper presents a novel method of generating multiple Fresnel hologram watermarks of three-dimensional objects. Firstly, the original watermark signal is used as the layers of the virtual three-dimensional object, and the encrypted watermark signal is generated in the form of complex noise by using both the region multiplexing tomography and the Fresnel double random phase coding method. Then, the spectrum of the watermark signal is conjugate symmetrically arranged and inverse Fourier transform is performed to obtain the real-valued watermark. The spectrum of the watermark signal is set to be in a non-interested region of the host spectrum to reduce their influence on the digital reconstruction of the host hologram. Finally, the encoded watermark signal is superimposed on the host hologram with a certain intensity. The original host hologram is not required during watermark reconstruction, and blind extraction is achieved. The reconstructed quick response (QR) code from the host hologram can be scanned and identified. The simulation results show that the proposed scheme has good invisibility and robustness to various types of image attacking operations such as filtering, joint photographic experts group (JPEG) compression, Gaussian noise, cropping, and rotation. The proposed method has good digital reconstruction quality for both host hologram and watermark when suffering attacks, and the QR code in the reconstruction plane has good scan recognition. Diffraction interference problem among different watermark layers is solved by the controllable post-processing of the watermarks with adjustable reconstruction and no interference, and the watermark restruction quality is improved. Furthermore, the application of virtual optics enriches the watermarking signal design method and enhances the security of the algorithm.