We present a strategically smart method to controllably synthesize and rapidly identify carbon nanotube (CNT) intramolecular junctions (IMJs). Ultralong, horizontally aligned, and defect-free single-walled carbon nanotubes (SWNTs) grown in a chemical vapor deposition system were used as structural carriers of IMJs. The trenched structures were employed into the synthesis processes to induce strains onto SWNTs that lie suspended across them. As a consequence, the nanotube lattice and electronic structures were altered and topological defects were generated, leading to the formation of IMJs in the vicinity of the edge of the trenches. Characterizations using in situ Raman spectroscopy verified the presence of IMJs and classified them as S-S junctions. Electrical transport measurements reviewed the rectifying behavior of the as-obtained IMJs. Other types of IMJs induced by tube-substrate and tube-tube interactions were also characterized by taking the advantages of trenched structure.