Zwitterionic modification of colloids with weak acids and bases represents a promising strategy in creating functional materials with tunable properties and modeling the self-organization of charged proteins. However, accurate incorporation of the dynamic dissociation or association of ionization groups known as charge regulation (CR) is often intractable in theoretical and computational investigations since charge redistribution and configuration need to be evolved self-consistently. Using hybrid Monte Carlo and molecular dynamics simulations, we demonstrate that a dilute suspension of overall charge-neutral zwitterionic Janus nanoparticles shows a conformational transition from an open assembly of string or bundle to compact cluster along with the variation in pH. The behavior under CR is qualitatively different from the commonly employed constant charge condition where the transition is absent. The CR-induced clustering is due to the inhomogeneous and fluctuating charges localized near the equatorial boundary of the Janus particle. These features are enhanced particularly at low salt concentration and high electrostatic coupling strength. Our results indicate the critical role of charge regulation in the spatial self-organization of zwitterionic nanoparticles.