Photo-thermo sensitive male sterile (PTMS) line is one of the important materials in utilizing heterosis in crops. Wheat line BNS (Bainong sterility) is an important nuclear-controlling PTMS line and suitable for growing and seed production in Huang Huai wheat zone in China. It has genetic stability with male sterility when sowing in autumn and male fertility when sowing in spring. Their thermosensitive periods were between stamen and pistil differentiation stage and anther connective stage and they could be regarded key periods for fertility conversion in BNS. To determine the molecular mechanisms of fertility conversion at thermosensitive period, we investigated characters of seed setting, anther and pollen grain of fertile and sterile BNS plants and compared young spike proteome patterns at their thermosensitive periods between the two BNS plants. The results showed that sterile plants had lower seed setting rate and pollen number, small pollen grain and lower pollen vitality than fertile plants. Out of protein spots reproducibly detected and analyzed on two dimensional electrophoresis gels, 76 spots showed significant changes in at least one BNS plant and 36 spots were identified by MALDI-TOF MS. The results showed that proteins involved in multiple biochemical pathways were differentially expressed at thermosensitive period between the two plants, including energy metabolism, stress response, signal transduction and regulation, protein process, amino acid and fatty acid metabolism, nucleic acid metabolism etc. Some of these proteins are reported to be involved in the abortion of anther or pollen grains in MS plants, such as energy metabolism and anti oxidative stress, and some were found to be novel proteins involved in the fertility conversion, such as phytohormones regulation. These results indicated that proteins related with anther or pollen development had expressed differently between the two BNS plants before anther development and phytohormones and signal transduction might be involved in the regulation of fertility conversion at thermosensitive period. Our studies have provided new insight to reveal the molecular mechanisms of fertility conversion at thermosensitive period in PTMS wheat.