This study aims to overcome the technology difficulties, especially considering the stability of the borehole of the reservoir formation when drilling in marine natural gas hydrate (NGH) bearing deposit under low temperature conditions and to develop the suitable working fluids using the calcium-Based bentonite clay (Ca-Bt) modified in the presence of nanosilica. It is found that the Ca-Bt modified by nanosilica (nano-Bt) has the higher moisture adsorption capability, the mud yield, and the cation exchange capacity (CEC) than sodium-based bentonite (Na-Bt) as well as the most suitable ratio of the amounts of nanosilica to Bt was gotten, which is helpful for the determination of nano-Bt clay modification. The comparing evaluation experimental tests of the drilling fluids show that the formulae using nano-Bt instead of Na-Bt have the higher viscosities (AV and PV), lower filtration loss (FL), and the almost same densities. Furthermore, the optimal fluid formulae using nano-Bt for low temperature marine NGH formation drilling were obtained as: Nano-Bt (1.2 wt%) + PEG (2 wt%) + NaCl (2 wt%) + CaCO3 (0.05 wt%) + Lv-CMC (0.5 wt%), with AV of 26.8 mPa·s, PV of 24.6 mPa·s, density of 0.992 kg/m3, FL of 9.1 ml and YP of 2.6. Moreover, the filtration films formed show the denser and the thinner (0.98 ± 0.1 mm) properties which implies the low solid phase content in the fluids could play the sufficient role in protecting the borehole of NGH bearing sediment from instability with the permeability decreasing to 1.97 × 10−2 μm2. Besides, the principle of the improvement of the characteristics of the bentonite clay modified by nanosilica was analyzed and a new structure of the flocculence-like with certain elastic characteristics on the surface of the Bt clay particles was proposed by observing the filtration films dried under 5000 times electron microscope, which provides the potential understanding for the effects on the drilling fluids films by nanosilica. This experimental tests results are expected to provide the modified bentonite clay materials with the new style structure and the reference of the circulation fluids formula for drilling and sampling in marine NGH bearing formation especially considering the stability of the borehole of deep sea reservoir sediment. •A new type bentonite clay was formed by nanosilica modification.•The super-thin filtration films were produced by modified clay.•A new flocculence-like structure on the surface of clay particles is proposed.