Background: Antinuclear antibodies (ANAs) are invaluable biomarkers for the diagnosis of autoimmune diseases (AIDs). This study aims to compare the performances of line immunoassay (LIA), multiplex bead-based flow fluorescent immunoassay (MBFFI), and magnetic bar code immunofluorescence assay (MBC-IF) to detect ANA-Profile-15S. Methods: In total, 184 samples from AID patients and 50 healthy controls (HCs) were collected. Fifteen ANAs (anti-dsDNA, nucleosome, histone, Sm, PCNA, ribosomal-P, SS-A/Ro52, SS-A/Ro60, SS-B/La, centromere B [CENP-B], Scl-70, U1-snRNP, AMA-M2, Jo-1, and Pm/Scl) were subjected to parallel detection by the LIA, MBFFI, and MBC-IF. The consistency between assays was analyzed. The discrepant results were further examined by chemiluminescent immunoassay (CLIA). Results: Anti-SS-A/Ro52 and SS-A/Ro60 autoantibodies were the most common autoantibodies in ANA positive-profiles, and were detected with equal efficiency by the LIA, MBFFI, and MBC-IF (p = 0.101 and p = 0.732, respectively). The three assays showed excellent agreement (consistency range: 66.5%-97.5%), and total consistency was 85.8%. The MBFFI and MBC-IF assays were in good agreement in terms of ANA-Profile-15S determination; the kappa coefficient ranged from 0.59 to 0.95, except for the PCNA and PM-Scl. Of the 262 re-assessed divergent results, 124 (47.33%) were positive on CLIA; the various autoantibodies exhibited variable patterns. More importantly, the ANA-Profile-15S results of the MBFFI and MBC-IF accurately identified patients with AID; the area under the curves ranged from 0.642 to 0.919. Conclusions: The novel MBFFI and MBC-IF assay performed well in detecting ANA-Profile-15S. The application of MBFFI and MBC-IF play important roles in laboratory diagnosis of AIDs.