Spatial control of prokaryotic cell division is flexible and diverse, but solely achieved by directing Z-ring assembly at specified position. In E. coli, pole-to-pole oscillation of Min proteins, together with nucleoid occlusion (NO), destabilize Z-ring assembly away from midcell to ensure faithful septation. The Min oscillation, via the interplay of MinD-ATPase and its activator MinE on the membrane, establishes a time-averaged MinCD gradient, thereby yielding a pronounced minimum of MinC’s inhibition on Z-ring assembly at midcell. Because the early-division proteins ZipA and ZapAB, along with FtsZ, assemble into complexes counter-oscillating with respect to MinC, stable oscillation to suppress Z-ring assembly is expected to allow MinC residing in each polar zone longer than the half-time of FtsZ turnover. While the Min oscillation has been displayed by synthetic minimal systems, it is unclear the interplay of Min proteins and compartment geometry are sufficient to bolster oscillating stability in vivo. Here we show that the Min-nucleoid interaction is the physicochemical element missing in previous researches to commit stable oscillations of Min proteins. We found in anucleate and nucleoid-perturbed cells that the Min oscillation is deviated up to a quarter-cycle, but oscillation frequency either goes up in anucleate and down in nucleoid-perturbed cells. Intriguingly, improved stability and reduced frequency are observed in cells expressing NO factor SlmA higher than native level. Our results reveal an unanticipated role of the nucleoid in modulating frequency and stability of cellular Min system and SlmA is indicated to facilitate such modulations. We propose a fresh perspective that frequency-modulation of Min system is mediated through the act of nucleoid-associated factor(s), and envision a sophisticated model of Min-nucleoid interaction ascribing to SlmA-facilitated conversion of physicochemical states in MinE dimer.