To investigate the intra- and inter-limb muscle coordination mechanism of human hands-and-knees crawling by means of muscle synergy analysis, surface electromyographic (sEMG) signals of 20 human adults were collected bilaterally from 32 limb related muscles during crawling with hands and knees at different speeds. The nonnegative matrix factorization (NMF) algorithm was exerted on each limb to extract muscle synergies. The results showed that intra-limb coordination was relatively stable during human hands-and-knees crawling. Two synergies, one relating to the stance phase and the other relating to the swing phase, could be extracted from each limb during a crawling cycle. Synergy structures during different speeds kept good consistency, but the recruitment levels, durations, and phases of muscle synergies were adjusted to adapt the change of crawling speed. Furthermore, the ipsilateral phase lag (IPL) value which was used to depict the inter-limb coordination changed with crawling speed for most subjects, and subjects using the no-limb-pairing mode at low speed tended to adopt the trot-like mode or pace-like mode at high speed. The research results could be well explained by the two-level central pattern generator (CPG) model consisting of a half-center rhythm generator (RG) and a pattern formation (PF) circuit. This study sheds light on the underlying control mechanism of human crawling.