The present study is concerned with a theoretical analysis of the photophoresis of a microsized long cylinder in a perpendicular optical field. Different from previous studies of photophoresis, thermal stress slip usually neglected is taken into account in the analysis. The gaseous fluid relative to the microparticle in photophoretic motion falls into slip-flow regime. Asymmetric distribution of the absorbed heat energy within the particle becomes the driving force for photophoretic motion of the cylinder-shaped particle. By evaluating heat source function distributions at various conditions, the study focuses on the effects of particle size and optical properties on the energy distribution and the resultant influences on the photophoresis. The photophoretic mobility is developed by the slip flow model with consideration of thermal stress slip. The results reveal that the photophoretic mobility decreases with the increase of particle thermal conductivity (k*) and increases with Knudsen number (Kn). The thermal stress slip effect on photophoretic velocity is more noticeable at high Kn, but disappears at the continuum limit. A long cylinder-shaped particle has higher photophoretic velocity than a spherical particle at low k*, while the situation reverses at high k*. With thermal stress slip considered, the critical condition for crossing of the photophoretic velocity curves of cylindrical and spherical particles is mildly influenced by Kn.