Natural microalgae (NA, cyanobacteria) collected from Taihu Lake (Jiangsu, China) were used for biofuel production through pyrolysis. The microalgae were de-ashed via pretreatment with deionized water and hydrochloric acid, and the samples obtained were noted as 0 M, 0.1 M, 1 M, 2 M, 4 M, 6 M, 8 M, respectively, according to the concentration of hydrochloric acid used in the pretreatment. Pyrolysis experiments were carried out at 500 °C for 2 h. The products were examined by various techniques to identify the influence of the ash on the pyrolysis behavior. The results showed that the ash inhibited the thermal transformation of microalgae. The 2 mol/L hydrochloric acid performed the best in removing ash and the liquid yield increased from 34.4% (NA) to 40.5% (2 M). Metal-oxides (mainly CaO, MgO, Al2O3) in ash promoted the reaction of hexadecanoic acid and NH3 to produce more hexadecanamide, which was further dehydrated to hexadecanenitrile. After acid pretreatment, significant improvement in the selectivity of hexadecanoic acid was observed, ranging from 22.4% (NA) to 58.8% (4 M). The hydrocarbon compounds in the liquid product increased from 12.90% (NA) to 26.67% (2 M). Furthermore, the acid pretreatment enhanced the content of C9–C16 compounds and the HHV values of bio-oil. For natural microalgae, the de-ashing pretreatment before pyrolysis was essential for improving the biocrude yield and quality, as well as the biomass conversion efficiency.