This paper describes the atmospheric correction algorithm for the Airborne Multi-angle TIR/VNIR Imaging System (AMTIS) in VIS/NIR bands. The method is named as a BRDF loop based algorithm. Under the assumption of that the ground cover is non-Lambertian, MODTRAN4 is used to calculate the atmosphere parameters, and the parameters used to decouple the multi-bouncing effect such as direct-hemisphere reflectance and hemisphere-direct reflectance are estimated in the loop correction process. The BRDF model used to calculate albedo is the kernel-driven model. To accelerate the atmospheric correction, all the atmospheric parameters used in this algorithm are pre-computed used MODTRAN4.1 and saved in the look-up table. A prior knowledge is used in the inversion of kernel-driven model when the multi-angle sampling is not enough. The atmospheric correction result is validated using the synchronous ground measurements. From the comparison with the general Lambert assumption based method, it is found that our BRDF loop based method can partly remove the atmospheric smoothing effect.