The key innovation in Hadamard transform spectral imager (HTSI) introduced recently is the use of digital micro-mirror device (DMD) to encode spectral information. However, it brings some new problems for us to solve synchronously. An interlaced encoding phenomenon caused by the application of DMD to our HTSI was investigated and analyzed. These interlaced encoding pixels were not encoded based on Hadamard transform; therefore they should be processed specially in spectrum recovery. To improve the quality of the recovered spectral images, a positioning method and a decoding method for the interlaced encoding pixels were proposed. In our experiment, we first directed a beam of laser into our HTSI to fill the field of view and labeled the positions of the interlaced encoding pixels. Then we recorded two groups of the encoded images of the target by changing the positions of all the encoding channels on the DMD. The interlaced encoding pixels could be distinguished easily by observing the number of non-zero constants and zero elements in a column vector which is made up of the gray values of a pixel of the encoded images in sequence. The interlaced encoding pixels of the first group of the encoded images turned into the normal Hadamard encoding pixels of the second group of the encoded images. The interlaced encoding pixels of the first group of the encoded images can be decoded through applying inverse Hadamard transform to the corresponding pixels of the second group of the encoded images. The experimental results prove the feasibility of the decoding method.