Transcranial focused ultrasound (tFUS) possesses significant advantages such as non-invasiveness and high tissue penetration depth, making it a promising tool in the field of brain science. Acoustic holographic lenses can manipulate the sound field through phase modulation, providing a low-cost and convenient approach for realizing transcranial focusing. Acoustic holographic lenses have been successfully utilized for achieving precise transcranial focusing in living mice to open the blood-brain barrier and for performing neural modulation, which shows considerable application potential. However, existing transcranial acoustic holographic lenses can only be driven by specific ultrasound frequencies and focused at predetermined positions, which limits their flexibility in complex applications. To address this issue, this study establishes a multi-frequency transcranial focusing method based on acoustic holographic lenses to enhance its adaptability in the field of tFUS. By integrating acoustic holographic lenses designed for different focal positions at various frequencies, we generate multi-frequency acoustic holographic lenses suitable for transcranial focusing and conduct experiments to evaluate their performance. In simulations, for single-focus tasks, the peak signal to noise ratio(PSNR) of the proposed method achieves 32.16 dB under 1 MHz ultrasound excitation, and 40.18 dB and 2 MHz ultrasound excitation, respectively; for multi-focus tasks, the PSNR values are 29.39 dB and 39.89 dB, respectively. In experiments, for single-focus tasks, the PSNR value of the proposed method is 27.48 dB under 1 MHz ultrasound excitation, and 32.33 dB under 2 MHz ultrasound excitation, respectively; for multi-focus tasks, the PSNR values are 23.30 dB and 32.17 dB, respectively. These results demonstrate that the multi-frequency transcranial acoustic holographic lens can effectively modulate the sound field under varying ultrasound frequencies and create high-quality focal points at different locations behind the skull, which significantly enhances the application flexibility of transcranial acoustic holographic lenses.