Alginate oligosaccharides (AOS) showed various biological activities. Traditional protocol for producing AOS was a multiple-step and high-pollution procedure. In this study, a rapid and efficient AOS producing method was developed directly from Laminaria japonica. Natural sun-dried L. japonica with a feed ratio of 1:7 (w/v) was pretreated using cellulase with a dry weight of 3%, for releasing the fermentable sugars (8.5 g/L glucose and 15.2 g/L mannitol). Then, the engineered yeast Yarrowia lipolytica strain with alginate lyase activity was grown using an algae-based medium. After fermentation for 72 h, glucose and mannitol were completely consumed, and 71.8 mM AOS was extracted from the fermentation supernatant. The degree of polymerization (DP) was ranging from 2 to 3. The recovery yield of AOS was about 91.7%. The purity of the extracted AOS was 92.6%. Overall, our work provided new insights for the development of green biotechnologies for oligosaccharide production from seaweed.