Focusing on the issue of low efficiency of SKINNY encryption algorithm in Central Processing Unit(CPU), a fast implementation method was proposed based on Graphic Processing Unit(GPU). In the first place, an optimization scheme was proposed by combining the structural characteristics of SKINNY algorithm, and one whole calculation, where the whole calculation was integrated by 5 step-by-step operations. Moreover, the characteristics of the Electronic CodeBook(ECB) mode and counter(CTR) mode of this algorithm were analyzed, and the parallel design schemes such as parallel granularity and memory allocation were given. Experimental results illustrate that the efficiency and throughput of SKINNY algorithm implemented by Computing Unified Device Architecture(CUDA) are significantly improved, when compared to the algorithm with the traditional CPU implementation. More specifically, for data size of 16 MB or large size, the SKINNY algorithm implementation with ECB mode achieves maximum efficiency improvement of 99.85% and maximum speedup ratio of 671. On the other hand, the SKINNY algorithm implementation with CTR mode achieves maximum efficiency improvement of 99.87% and maximum speedup ratio of 765. In particular, the throughput of the proposed SKINNY-256(ECB) parallel algorithm has 1.29 times and 2.55 times of those of the existing AES-256(ECB) and SKINNY_ECB parallel algorithms, respectively.