Pot experiments were carried out over two growing periods to assay the biocontrol efficacy and rhizosphere colonization of Trichoderma harzianum SQR-T037 (SQR-T037) applied as SQR-T037 conidia suspension (TCS), SQR-T037 conidia suspension blended with organic fertilizer (TBF), or SQR-T037 fermented organic fertilizer (TFF). Each formulation had three T. harzianum numbers. In two experiments, Percent Disease Indexes (PDIs) decreased with the increase of SQR-T037 number added to soils. The TFF treatment consistently exhibited the lowest PDIs at same amendment rate of SQR-T037 and 0–8.9%, 25.6–78.9%, and 4.4–50.0% of PDIs were found in TFF, TCS, and TBF treatment, respectively. Soils treated with TFF showed the highest SQR-T037 population in rhizosphere and bulk soil. Decrease of Fusarium oxysporum population in both bulk and rhizosphere soils occurred in the treatment SQR-T037 at 105 and 106 cfug−1 soil rate. The TFF treatment at the SQR-T037 rate of 103 cfug−1 soil significantly (p < 0.05) increased SQR-T037 population within the rhizoplane but had no effect on F. oxysporum population when compared to TCS and TBF. Generally, TFF treatments were superior to TCS and TBF treatments on disease control by sustaining colonization of SQR-T037 and decreasing F. oxysporum abundance in the rhizosphere soil. We propose that TFF treatment at SQR-T037 rate of 107 cfug−1 (i.e., 105 cfug−1 soil after applied to soil) was the best formulation for controlling Fusarium wilt of cucumber.