Currently, low heat Portland (LHP) cement is widely used in mass concrete structures. The magnesia expansion agent (MgO) can be adopted to reduce the shrinkage of conventional Portland cement-based materials, but very few studies can be found that investigate the influence of MgO on the properties of LHP cement-based materials. In this study, the influences of two types of MgO on the hydration, as well as the shrinkage behavior of LHP cement-based materials, were studied via pore structural and fractal analysis. The results indicate: (1) The addition of reactive MgO (with a reactivity of 50 s and shortened as M50 thereafter) not only extends the induction stage of LHP cement by about 1–2 h, but also slightly increases the hydration heat. In contrast, the addition of weak reactive MgO (with a reactivity of 300 s and shortened as M300 thereafter) could not prolong the induction stage of LHP cement. (2) The addition of 4 wt.%–8 wt.% MgO (by weight of binder) lowers the mechanical property of LHP concrete. Higher dosages of MgO and stronger reactivity lead to a larger reduction in mechanical properties at all of the hydration times studied. M300 favors the strength improvement of LHP concrete at later ages. (3) M50 effectively compensates the shrinkage of LHP concrete at a much earlier time than M300, whereas M300 compensates the long-term shrinkage more effectively than M50. Thus, M300 with an optimal dosage of 8 wt.% is suggested to be applied in mass LHP concrete structures. (4) The addition of M50 obviously refines the pore structures of LHP concrete at 7 days, whereas M300 starts to refine the pore structure at around 60 days. At 360 days, the concretes containing M300 exhibits much finer pore structures than those containing M50. (5) Fractal dimension is closely correlated with the pore structure of LHP concrete. Both pore structure and fractal dimension exhibit weak (or no) correlations with shrinkage of LHP concrete.