This study (i) examined the formation of two major carbonaceous disinfection by-products (C-DBPs), trihalomethanes (THMs) and haloacetic acids (HAAs), during the chlorination of intracellular algogenic organic matter (IOM) extracted from two commonly blooming algae M. aeruginosa (MA) and Chlorella sp. (CH), and (ii) investigated the roles and relationships of fluorescent and molecular weight (MW) properties on/with IOM-derived THMs and HAAs. The extracted IOM samples were separated into different MW fractions by centrifugal devices with membrane support with MW cut-offs of 100, 30, 10, 3, and 1 kDa. We observed an overall reduction of C-DBPs with a decrease of IOM-MW from >100 kDa to <1 kDa. Of six fractionated IOM, a large fraction (>100 kDa) contributed the largest amount to the MW distribution of IOM, accounting for 33 and 42% of the total dissolved organic carbon (DOC) of MA and CH, respectively. It also had the highest-yielding potential to produce significant levels of THMs and HAAs, and total C-DBPs over other small MW fractions. Although small MW fractions (>10 kDa) contributed around 50% of the total DOC, they made an insignificant contribution (>20%) to the THMs, HAAs, and overall C-DBPs. Furthermore, the decrease of IOM MW caused a shift from the domination of HAA formation to THM formation, especially when MW was <10 kDa. By canonical correspondent analysis, the relationship of IOM-derived THMs and HAAs with IOM properties was examined. In particular, large fractions of IOM, exhibiting aromatic protein- (AP) and soluble microbial product- (SMP) like fluorescence, are favorable for the formation of HAAs, whereas small MW fractions of IOM with HA- and FA-like fluorescence preferentially tends to form THMs. Our findings evidently show the strong dependence of IOM-derived THMs and HAAs on the fluorescent and MW properties. Therefore, the characterization of MW and fluorescent properties can provide the advantages in the control of algae-derived DBPs upon the chlorination of eutrophic water.