This study aimed to prepare gelatin–fucoidan microspheres with enhanced doxorubicin binding efficiency and controllable biodegradation using fish gelatin combined with low molecular weight (LMW) gelatin and fucoidan at fixed ratios. The MW of gelatin was modified by subcritical water (SW), which is known as a safe solvent, at 120 °C, 140 °C, and 160 °C. In addition, gelatin–fucoidan microspheres were prepared using a solvent exchange technique. Our findings revealed that particle size decreased, the surface was rougher, the swelling ratio increased, and particle shape was irregular in microspheres composed of SW-modified gelatin. Doxorubicin binding efficiency was improved by fucoidan and SW-modified gelatin at 120 °C but not at 140 °C and 160 °C. Interestingly, an increase in in vitro enzymatic degradation was observed in the microspheres consisting of SW-modified fish gelatin, although the cross-linking degree between them was not significantly different. This is because LMW gelatin could form more cross-linked bonds, which might be weaker than the intramolecular bonds of gelatin molecules. Gelatin–fucoidan microspheres consisting of SW-modified fish gelatin with controlled biodegradation rates could be a candidate for a short-term transient embolization agent. In addition, SW would be a promising method to modify the MW of gelatin for medical applications.