The invention discloses a polymer micro-channel machining method based on space-time shaping femtosecond laser, and belongs to the field of laser application. The method comprises the following stepsthat step 1, a polymer substrate sample is prepared as a to-be-machined sample; step 2, repeat frequency of femtosecond laser monopulse is set as 10-20 Hz, and space-time shaping parameters are set that femtosecond laser monopulse shaping is modulated to be 1-3 pulse sequences, wherein each of the pulse sequences is composed of two sub-pulses, delay time between the two adjacent sub-pulses is -5ps-5ps, sub-pulse energy ratio is 1:1 or 2:1, total pulse energy is 30-50 muJ, and the distribution of sub-pulse light field is Bessel distribution; and step 3, according to the parameters, monopulse femtosecond laser is modulated as a space-time shaping double-pulse laser sequence, and the double-pulse laser sequence is focused on the surface of the to-be-machined sample prepared in the step 1 to form the polymer micro-channel by vertical machining. Local transient electron dynamics in material machining is effectively controlled by the space-time shaping, quality of the prepared polymer micro-channel is improved by vertical machining, and repeatability is high.