According to the capacity of multi-level caches, the population individuality and ant data in CPU main memory were assigned to L3 cache, L2 cache and L1 cache to reduce data transfer overhead among multiple caches during parallel computing. The asynchronous and incomplete transmission was performed between CPU and GPU, and multiple flows were asynchronously executed by multiple GPU kernel functions. The thread number of GPU block was set to the size of 16 times and GPU public memory was divided into bank with the size of 32 times. GPU constant memory was used to store read-only parameters such as cross probability and mutate probability which were read frequently. The read-only big data structure such as string set and overlap matrix were bound to GPU texture memory, and a computation, cache and communication-efficient parallel algorithm for CPU and GPU to coordinate solving shortest common superstring problem was designed and implemented. The experimental results for solving shortest common superstring problem with several sizes show the proposed CPU and GPU parallel algorithm is faster over 70 times than the sequential algorithm.