Mesoporous silica nanoparticles (MSNs) are of growing interest for the development of novel probes enabling efficient tracking of cells in vivo using magnetic resonance imaging (MRI). The incorporation of Gd3+ paramagnetic ions into highly porous MSNs is a powerful strategy to synthesize “positive” MRI contrast agents for more quantitative T1-weighted MR imaging. Within this context, different strategies have been reported to integrate Gd chelates to 2D pore network MSNs. As an alternative, we report on the modulation of the pore network topology through the preparation of a 3D pore network hybrid GdSixOy MSN system. In this study, 2D GdSixOy-MSNs with similar porosity and particle size were also prepared and the relaxometric performances of both materials, directly compared. Both syntheses lead to water-dispersible MSNs suspensions (particle size < 200 nm), which were stable for at least 48h. 3D GdSixOy-MSNs provided a significant increase in 1H longitudinal relaxivity (18.5 s−1mM−1; 4.6 times higher than Gd-DTPA) and low r2/r1 ratios (1.56) compatible with the requirements of “positive” contrast agents for MRI. These results demonstrate the superiority of a 3D pore network to host paramagnetic atoms for MRI signal enhancement using T1-weighted imaging. Such an approach minimizes the total amount of paramagnetic element per particle.