This study used semi-thin sectioning and cytochemistry to investigate the relationship between pollen nutrient metabolism and pollen abortion in male sterile lines of wheat induced by SQ-1 (a chemical hybridising agent). Anthers were collected from the tetrad to trinucleate stages, and 4′ ,6-diamidino-2-phenylindole staining was used to visualise nuclei and confirm the development stage. Sudan Black B, periodic acid–Schiff, Coomassie Brilliant Blue, and toluidine blue were used to detect lipids, starch, proteins, and acidic polyanions, respectively. Semi-thin sectioning indicated that nutrient accumulation was much higher in the fertile line 1376 than in the sterile line 1376-PHYMS. Further, no lipids were found in the free microspore stage in the sterile line; however, at the late microspore stage, more proteins and acidic polyanions were found in the sterile line 1376-PHYMS pollen than in the fertile line 1376 pollen. From the binucleate to trinucleate pollen stages, the starch content was low and the intine considerably thinner in the pollen of the 1376-PHYMS line. SQ-1 probably hampered nutrient metabolism in the anthers, leading to decreased nutrient supply and abnormal intine formation, ultimately resulting in pollen abortion. A new mechanism for nutrient absorption, i.e. endocytosis of Ubisch bodies or orbicules by the intine through the germinal aperture, was revealed.