In this work, the thermal imidization of 3,3′, 4,4′-biphenyltetracarboxylic dianhydride/p-phenylenediamine (BPDA/PDA), pyromellitic dianhydride/4,4′-oxydianiline (PMDA/ODA), 4,4′-oxydiphthalic anhydride/4,4′-oxydianiline (ODPA/ODA), and 4,4'-(hexafluoroisopropylidene)diphthalic anhydride/2,2′-bis(trifluoromethyl)benzidine (6FDA/TFMB) polyimides (PIs) were investigated based on molecular dynamics (MD) simulation. It was found that two kinds of imide bonds were formed, i.e., inter-molecular and intra-molecular imide bonds, which results in differences in the final architecture of the target PI systems. The BPDA/PDA and PMDA/ODA PIs present crosslinking network structure, while the ODPA/ODA PI shows a hybrid structure composed of crosslinking and linear fragments, and the 6FDA/ODA PI displays linear and branched structures. Compared with the previous view of linear PI molecular chains, these results agree well and better account for the thermoset of PMDA/ODA and BPDA/PDA, thermoplasticity of ODPA/ODA, and solubility of 6FDA/TFMB. The mechanism causing the above differences was studied from radial distribution function (RDF), coordination number, fractional free volume (FFV), and density field analysis. By comparing the experimental and simulated values of glass transition temperature and modulus of PI models, the rationality of inter-molecular imide bonds is proved. In addition, through the PAA/DMF compound models, it was found that the increase of solvent content hindered the formation of inter-molecular imide bonds. This study provides new insights into the thermal imidization process and the final architecture of PIs derived from poly(amic acid).