A series of nanocomposites based on a new semi-crystalline polyimide (PI) and multi-walled carbon nanotubes (MWCNTs) were prepared by in situ polymerization. The TEM measurement reveals the improved dispersion of carboxylic acid-functionalized MWCNTs (COOH-MWCNTs) in semi-crystalline PI compared with pristine MWCNTs. The TGA analysis show that the concentration of carboxylic acid groups on the surface of nanotubes is about 4.34 wt%. The FT-IR spectroscopy analysis indicate that the imide rings of the PI interact non-covalently with nanotubes. The Polarized optical microscopy observation reveals significant morphology evolution in semi-crystalline PI induced by MWCNTs. The SEM micrographs suggest the strong interfacial interaction between COOH-MWCNTs and PI main chains, and significant changes in the fracture surfaces morphology. The WAXRD measurements reveal that COOH-MWCNTs promote the semi-crystalline PI crystallinity and structure change. COOH-MWCNTs can more efficiently improve the mechanical and thermal properties of resulting nanocomposites than pristine MWCNTs. COOH-MWCNT/PI nanocomposites show increases of Young's modulus and yield strength, as high as 20-30 %, without sacrificing the elongation at break at loadings of 0.5 wt% nanotubes. Furthermore, with increasing the loadings of COOH-MWCNTs to 1.0 wt%, Young's modulus and yield strength decrease due to nanotube aggregation, but elongation at break increase about 46 %. An abrupt increase of elongation at break in pristine MWCNT/PI nanocomposites was also registered at nanotubes loadings increasing from 0.5 to 1 wt%. These results indicate that the properties of semi-crystalline PI nanocomposites reinforced with carbon nanotubes are not only determined by the dispersion of nanotubes in the PI matrix and their interfacial interactions, but also by the crystalline phase morphology evolution in the PI matrix.