Brown seaweed (Sargassum polycystum) contains fucoxanthin that has efficacy as antioxidant and antiobesity. The difference from physicochemical of sodium trypolyphosphate as synthetic cross-linker and sodium alginate as natural cross-linker gives the difference of nanoparticles size, and extract’s dissolving increase if there is particle size reduction. This study aims to determine different characteristic of nanoparticles and concentration of fucoxanthin using sodium trypolyphosphate and sodium alginate as cross-linker. Brown seaweed is extracted by kinetic maceration, brown seaweed extract is made into nanosuspension. Preparation of nanosuspension is using gelation ionic method and the formation of nanosuspension are using chitosan as polymer with cross-linker sodium trypolyphosphate sodium alginate 0,1; 0,2; 0,3%. Nanosuspension characterization are particle size and zeta potential, after that nanosuspension dried up with freeze drying method, and nanoparticles characteristic are determine as nanoparticles morphology and fucoxanthin concentration using thin layer chromatography-densitometry. The results of nanoparticles characteristic using sodium trypolyphosphate and sodium alginate are particle size 297,5 nm and 164,7 nm, zeta potential 37,5 mV and 13,43 mv, nanoparticles morphology are net and spheric, with fucoxanthin concentration are 3,86% and 22,66%. Based on the results of those nanoparticles characteristic, the best nanoparticles is nanoparticles with sodium alginate as cross-linker. There are difference on nanoparticles characteristic using sodium trypolyphosphate and sodium alginate, and the results of statistical analysis with ANOVA one direction is p-value < 0,05.