We report novel methods for detection of hepatitis B surface antigen (HBsAg) based on competitive and sandwiched magnetic immunoassays using functional magnetic nanoparticles in a thin channel. Magnetic nanoparticles labeled with hepatitis B antibody are flowed through a thin channel to form a predeposition layer for capturing HBsAg. Competitive and sandwiched magnetic immunoassays were studied and detection limit, linear range, and sample selectivity were compared. The detection limits of competitive and sandwiched magnetic immunoassays were found to be 0.26 and 0.25 pg/ml, respectively. The linear range of HBsAg concentration was 0.26 pg/ml-2.6 ng/ml for competitive magnetic immunoassay and was 0.89 pg/ml-8.9 ng/ml for sandwiched magnetic immunoassay. The advantages of these methods over ELISA and other methods for HBsAg detection are lower detection limits and wider linear ranges. The running time was less than 30 min. Competitive magnetic immunoassay was faster than sandwiched magnetic immunoassay for detection of HBsAg. The measurements of HBsAg in serum samples from these methods differed by about 10% from those of ELISA. These methods can provide simple, fast, and sensitive detections of biomarkers and other immunoassay-related samples.