Ionospheres over sea areas have an inevitable impact on maritime-satellite communications; however, due to geographic constraints, ionospheric observation and analysis over sea areas are far from adequate. In our paper, slant total electron content (STEC) along small-satellite constellation-automatic identification system (AIS) signal rays is used for computerized ionospheric tomography (CIT) over sea areas, and small-satellite constellations can provide more effective signal rays than a single satellite. An adjustment factor delta is introduced to optimize the initial electron density for the multiplicative algebraic reconstruction technique (MART). The CIT results reconstructed by a traditional MART and our new method at 00:00 and 06:00, 15 March 2022, are compared, and our new method produces about a 15% and over 40% improvement in average deviation (AD) and root-mean-square error (RMSE). The results show that the bigger the difference between delta and 1, the better improvement will be in the 3D CIT process. The initial electron density is well selected during CIT when delta is approximate to 1, which is the case at 12:00, and the reconstructed 3D electron density, applying the initial ne and the adjusted initial ne, are both close to the true electron density. The small-satellite constellation-AIS signals are valuable resources for electron density reconstruction in sea areas.