ABSTRACTChemically‐interfered male sterility (CIMS) system in wheat (Triticum aestivum L.) is one of the male sterility types used for hybrid wheat production in China. The main morphological defect in male sterile line 1376‐CIMS interfered by chemical hybridizing agents (CHA) is that the tapetum seems to be abnormally degrated and pollen extine is aberrant. As a complex pollen wall in wheat, the pollen outer wall mainly contains lipidic sporopollenin. However, the mechanism for synthesizing these aliphatic precursors during pollen development has not been fully elucidated. To elucidate the relationship between aliphatic mechanism and chemically‐interfered male sterility, we report on the function of SQ‐1 (a new kind of chemical hybridizing agent) in aliphatic metabolism and its disruptive role during wheat pollen development. The observations of scanning electron microscopy revealed that anther and pollen wall formation was significantly altered in 1376‐CIMS. The contents of aliphatic compositions of anther underwent changes in 1376‐CIMS revealed by gas chromatography–mass spectrometry (GC–MS), including in particular reductions in fatty alcohols, alkanes and alkenes, and an abnormal increase in fatty acids in 1376‐CIMS. cDNA‐AFLP data revealed that an array of genes implicated in a diversity of biological pathways (180 in total, 124 up‐expression and 56 down‐expression) exhibited statistically significant expressional differences between 1376 and 1376‐CIMS. Also, a group of genes putatively involved in aliphatic transport and metabolism were significantly altered in 1376‐CIMS, indicating the disruptive role of SQ‐1 in aliphatic transport and metabolism in the formation of the anther and pollen wall. In addition to its function in promoting tapetum programmed cell death (PCD), SQ‐1 probably plays crucially perturbative roles in several basic biological processes during wheat anther development.