Basketball victory relies on an athlete’s skill to make precise shots at different distances. While extensive research has explored the kinematics and dynamics of different shooting distances, the specific neuromuscular control strategies involved remain elusive. This study aimed to compare the differences in muscle synergies during basketball shooting at different distances, offering insights into neuromuscular control strategies and guiding athletes’ training. Ten skilled shooting right-handed male basketball players participated as subjects in this experiment. Electromyographic (EMG) data for full-phase shooting were acquired at short (3.2 m), middle (5.0 m), and long (6.8 m) distances. Non-negative matrix decomposition extracted muscle synergies (motor modules and motor primitives) during shooting. The results of this study show that all three distance shooting can be broken down into three synergies and that there were differences in the synergies between short and long distances, with differences in motor primitive 1 and motor primitive 2 at the phase of 45% - 59% (p < 0.001, t* = 4.418), and 78% - 88% (p < 0.01, t* = 4.579), respectively, and differences in the motor module 3 found in the differences in muscle weights for rectus femoris (RF) (p = 0.001, d = -2.094), and gastrocnemius lateral (GL) (p = 0.001, d = -2.083). Shooting distance doesn't affect the number of muscle synergies in basketball shooting but alters synergy patterns. During long distance shooting training, basketball players should place more emphasis on the timing and synergistic activation of upper and lower limbs, as well as core muscles.