Optical aberrations caused by the scattering of biological tissues limit the imaging performance of optical systems. A near-infrared II fluorescence confocal imaging technique based on indirect wavefront shaping was investigated. First, we synthesized a highly efficient near-infrared II range fluorescent probe, where reducing the scattering of biological tissue can realize biopsy imaging with high-contrast. Second, we investigated the adaptive optical method based on indirect wavefront measurement. The indirect wavefront shaping technology was applied to the laser scanning confocal system, enabling the measurement and compensation of optical aberrations caused by biological tissues, and obtaining imaging of biological tissues with a high signal-to-noise ratio. Finally, near-infrared II fluorescence confocal imaging system based on indirect wavefront shaping was deployed and relevant experiments were conducted. The experimental results indicate that the system effectively compensates for the aberrations induced by air plates, scattering media and mouse skull, and increases the final signal intensity by 1.47, 1.95 and 2.85 times, respectively. As a result, the final imaging quality is significantly enhanced.