A series of azobenzene-containing side chain liquid crystalline polymers with various spacer lengths (pXMAN, where X, the number of methylene units, varies from 4 to 12) have been synthesized and characterized. Phases and aggregation have been studied by UV-visible spectroscopy as a function of temperature. Polarized spectra were measured before and after irradiation with a resonant pump light at 488 nm. The annealing process on polymers with short spacers (p4MAN-p8MAN) induces a hypsochromic shift while, for longer spacers (p9MAN-p12MAN), it induces a large bathochromic shift. These effects may be due to the strong dipolar interaction and interdigitation of the side chain chromophores in an antiparallel orientation. The irradiation of such organized films with either circularly or linearly polarized light induces a bathochromic shift by breaking the antiparallel organization. This is a consequence of the angular reorientation of the azobenzene moieties as a result of trans-cis photoisomerization. To estimate the orientation of the side chain azobenzene photoactive group, of the aliphatic spacer and of the main chain, linear dichroism in the infrared spectral range was measured using the polarization-modulation technique with in situ irradiation. From these experiments, a high and stable value of photoinduced linear dichroism reveals a strong interaction and self-organization of azobenzene side chain molecules during the relaxation process. The anisotropic reorientation of the polymer main chain and of the spacer is small when compared to the reorientation of the azobenzene side chains, which become perpendicular to the linearly polarized pump beam. Additional birefringence measurements were carried out with in situ irradiation followed by a relaxation cycle for the whole series of polymers in various phases. The stability and the rate of the induced birefringence depend on the initial degree of organization within the thin film and on its thermal history. It is noteworthy that annealing can lead to a significant improvement of the birefringence level (+44%). The results obtained on photoinduced orientation and phase organization are correlated with the polymer properties.