In order to compare the scale penetrability and penetration mechanism of different bactericides，a simulated penetration experiment was conducted under the scale layer from the field，employing polyhexamethylene monoguanidine hydrochloride （PHMH） and glutaraldehyde as prototypes. The pore size distribution of scale samples was characterized by nitrogen adsorption-desorption method. Meanwhile，the charging property of scale layers in 3.5% NaCl solution was determined by dynamic light scattering technique. Standard curves for PHMH and glutaraldehyde in 3.5% NaCl solution were established at 506.7 nm and 232.2 nm，respectively. With the aid of self-made device and standard curves，the penetrations of PHMH and glutaraldehyde with time were monitored by ultraviolet spectrophotometer. The results showed that two scale samples on site were mainly composed of calcium carbonate and barium sulfate with an average pore size of 0.43 and 0.27 μm，respectively. The Zeta potentials showed a trend from positive to negative as the pH value of the solution increased. The corresponding isoelectric points were 4.14 and 4.56， respectively. After immersing two scale samples in NaCl solution，the interface showed negative charge with Zeta potential of -6.56 mV and -5.14 mV，respectively. After 15 days of penetration monitoring，PHMH showed a slow penetration behavior first and then fast with 17.70% the highest permeability，while glutaraldehyde showed a fast penetration behavior first and then slow with 38.75% the highest permeability. The pore size of scale sample directly affected the total diffused amount of bactericide，but did not change its diffusion pattern. Electrostatic interaction with the scale layer resulted in the early slow penetration of PHMH，while physical screening effect determined the final penetration amount of glutaraldehyde. This work provided guidance for the screening of on-site bactericide and the synergistic compatibility with other agents.