This paper presents a systematic design of a high-efficiency magnetic resonant wireless power transfer (MR-WPT) system for biomedical implants based on the unconventional multisine (MS) transmission waveform. The MS waveform featuring a high peak to average power ratio can boost the system efficiency with an elaborate design. Optimizations on flexible coil, system model, and rectifier design are all considered to strengthen its efficiency improvement as well as eliminate its drawbacks. With all the proposed optimizations implemented, the MS waveform has been applied for the first time in practical MR-WPT system for in vivo power delivery. A 6.78-MHz MR-WPT system with 18-mm implant depth is realized for wirelessly powering a spinal cord stimulator. It achieves an overall system efficiency (both coils and rectifier included) of 50.7% with a three-tone 230-kHz tone spacing MS waveform postimplantation in the rodent model. Low specific absorption rate and the tissue temperature rising from electromagnetic fields in the body are also verified to guarantee a safe and practical wireless power link for biomedical implants.