Transposable element (TE) is a fragment of DNA sequences that can move and integrate into new sites to proliferate itself in the host genome. Based on this proliferation, TEs have been considered as "junk" or "selfish DNA". Most research has focused on investigating mechanisms of TE amplificationor silencing whereas the regulatory function of TEs has not been completely unraveled. Previous studies have suggested a positive correlation between genome size and TE content, which provides a basis for the interpretation of the C-value paradox. Emerging studies on the regulatory functions of TEs in the host genome have updated the concept of TEs as junk DNA. In plants, especially in crops, these studies have demonstrated that TEs can reshape the transcription of adjacent genes in cis or trans, consistent with the first characterization of TEs as "controlling elements". TEs can also create epialleles, which confer stress-inducible gene expression that can increase the sessile plant's environmental fitness. In this review, we summarize recent progress on functional studies of TEs andtheir significance for crop breeding in the future.