To further enhance the anti-interception performance of traditional weighted fractional Fourier transform (WFRFT) from the perspective of security of wireless communication system, the two-dimensional weighted fractional Fourier transform (2DWFRFT) was introduced. Based on the original one-dimensional transform, the kernel algorithm of 2DWFRFT further improved the anti-scanning property of the single-parameter WFRFT by taking advantage of multiple horizontal and vertical dimensional transforms with different parameters. First, the signal generation method was given, and the matrix expressions for specific cases were derived. Then, the implementation complexity of the proposed scheme and the advantages of constellation rotation characteristics were described. In order to fully illustrate the anti-interception performance of the scheme from the perspective of physical layer security information theory, the ergodic secrecy capacity was analyzed under the multiple-input single-output (MISO) wiretap channel model. Simulation results show that compared with the one-dimensional WFRFT, the order of 2DWFRFT consisted of multiple parameter vectors, which could effectively improve the interception resistance only at the cost of limited computational complexity, and provide richer constellation features by breaking the point limits of constellation scrambling. Finally, compared with the traditional artificial noise method, the proposed scheme had a higher security capacity without additional signal power consumption.