The invention provides a wellbore independent acidification method for a complex structural well. The method comprises: pulling out a production pipe string in a double-branched horizontal well; enabling a drifting gauge to reach to a branch well section horn mouth, washing the well for one and a half round; pulling out a drifting pipe string; connecting a branch well pilot tool with an oil pipe,lowering the pipe string to the branch well section horn mouth, raising and lowering an oil pipe seal to sealing a main wellbore, and aligning the window of the pilot tool with the branch wellbore window by rotating the pipe string; lowering a coiled tubing from the oil pipe to reach an upper branch wellbore through the pilot tool; injecting an acid solution into the upper branch wellbore from thecoiled tubing, soaking for appropriate time and exhausting the acid solution by inverse well flushing until the inflow and outflow solution have consistent property; pulling out the coiled tubing; raising the oil pipe to unseal the branch well pilot tool and pulling out the pilot tool to complete the acidification. The method solves the low efficiency of general acidification of the main wellboreand the re-pollution main wellbore.