As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities. Regulation of transposition is relatively complex and three factors such as maintaining structure for none- or cis- or trans-acting transposition, being controlled by the host genome and induction by biotic and abiotic stress may contribute altering its transposition activity. The important roles of retrotransposons to modify genome size, remodel genome structure, and displace gene functions in the plant genome have been proven by a growing number of research studies till date, which indicates that retrotransposons are important driving force in genome evolution. For this review, we summarized the latest theoretic and practical research progresses on plant retrotransposons for their distribution, regulation of activity, the impact on the architecture of plant genomes, and put forward the future prospects.