Three-dimensional (3D) single-particle tracking was employed to study the lipid membrane morphology change at different pHs on glass supported lipid bilayers (SLBs) [1,2-dioleoylsn -glycero- 3-phosphoethanolamine/1,2-dioleoyl-sn-glycero-3-phospho-L-serine (sodium salt)/1,2-dioleoyl-sn-glycero-3-phosphocholine = 5:3:2]. Fluorescently tagged, carboxylated polystyrene nanoparticles (of 100 nm) were used as the probes. At neutral pHs, the particles' diffusion was close to two-dimensional Brownian motion, indicating a mainly planar structure of the SLBs. When the environmental pH was tuned to be basic at 10.0, transiently confined diffusions within small areas were frequently observed. These confinements had a lateral dimension of 100-200 nm. Most interestingly, they showed 3D bulged structures protruding from the planar lipid bilayer. The particles were trapped by these 3D structures for a short period of time (similar to 0.75 s), with an estimated escape activation energy of similar to 4.2 k(B)T. Nonuniform distribution of pH-sensitive lipids in the membrane was proposed to explain the formation of these 3D heterogeneous structures. This work suggests that the geometry of the 3D lipid structures can play a role in tuning the particle-lipid surface interactions. It sheds new light on the origin of lateral heterogeneity on the lipid membrane.