In-situ passivation of soil chromium (Cr) contamination based on chemical and biological passivators has been widely concerned, however, the cooperative effect of two types of passivators on Cr passivation and soil properties was little investigated. In this study, nano zero valent iron (nZVI) and humic acid (HA) as the chemical passivators were selected and were combined with a novel Cr resistant strain QY-1 to study these two points. Results demonstrated that the combination was more effective in Cr immobilization, among which, HA + QY-1 had the highest passivation rate (82.83%), followed by nZVI + QY-1. HA + QY-1 alleviated soil Cr stress most efficiently as its soil relevant fertility indicators, microbial quantity, respiration and seed gemination rate significantly increased. On the contrary, nZVI decreased soil respiration and microbial abundance, but the addition of QY-1 could relieve this phenomenon. The results highlighted the ability of HA + QY-1 to remediate Cr contaminated soil and improve soil stability.