Usually, magnetic nanoparticles (MNPs) are prepared based on the famous Stöber process in which divinylbenzene (DVA) is often used as a crosslink agent to synthesize SiO2/(PMMA/Fe3O4) nanoparticles. Compared with DVA, linolenic acid (LNA) is innoxious and can polymerize more easily for it has three unsaturated double bonds. In this paper, LNA was used as a new crosslink agent instead of DVA to synthesize the SiO2/(PMMA/Fe3O4) nanoparticles. The results showed that the core-shell structure could be observed obviously. The sizes of nanoparticles with core-shell structure range from 200 to 500 nm. The DNA probes which was immobilized on the surface of MNPs were used to capture the biotin modified complementary sequence of the probe, and the formed complexes were bonded with streptavidin-modified alkaline phosphatase (SA-AP). Finally the chemiluminescent signals were detected by adding 3-(2'-spiroadamantane)-4-methoxy-4-(3"-phosphoryloxy) phenyl-1, 2-dioxetane (AMPPD) which was the substrate reagent of AP. The specificity and sensitivity of this approach were investigated in this paper.