Three kinds of partially deacetylated heterochitosans, 90% deacetylated chitosan, 75% deacetylated chitosan and 50% deacetylated chitosan, were prepared from crab chitin by N-deacetylation with 40% sodium hydroxide solution for different durations. Nine kinds of heterochitooligosaccharides (hetero-COSs) with relatively high molecular weights (5,000–10,000 Da; 90-HMWCOSs, 75-HMWCOSs, and 50-HMWCOSs), medium molecular weights (1,000–5,000 Da; 90-MMWCOSs, 75-MMWCOSs, and 50-MMWCOSs), and low molecular weights (below 1,000 Da; 90-LMWCOSs, 75-LMWCOSs, and 50-LMWCOSs) were prepared using an ultrafiltration membrane reactor system, respectively. In addition, their sulfated derivatives were prepared by a method using a trimethylamine-sulfur trioxide, and the anticoagulant properties of the heterochitosans and their COS sulfates with different chain lengths and degrees of deacetylation were investigated. Clotting times in thrombin-time assay were prolonged in the presence of various concentrations of the heterochitosans and their COS sulfates using normal human plasma. The 90% deacetylated chitosan sulfate exhibited the highest anticoagulant activity among all the heterochitosans and their COS sulfates.