Adding organic compounds to wastewater can improve the carbon/nitrogen ratio and benefit microalgae growth. We studied microalgal growth, nutrient removal and lipid accumulation of Chlorella pyrenoidosa cultured in a mixture of swine wastewater (SW) and furfural wastewater (FW). The mix ratio of SW:DFW (diluted furfural wastewater) had a significant effect on microalgae growth. As the mix ratio of SW:DFW decreased from 1:0.5 to 1:19, the maximum microalgal biomass increased, while the specific growth rate initially increased and then decreased. The efficiency of nutrient removal also depended on the mix ratio of wastewater. The highest chemical oxygen demand (COD) removal efficiency (57.30%) occurred at the mix ratio of SW:DFW = 1:3. The highest removal efficiencies of total phosphorous (TP) reached 61.93% when the mix ratio of SW:DFW was 1:9. Wastewater at the mix ratio of SW:DFW = 1:19 had a maximum lipid productivity of 49.48 mg L−1 d−1, which was 4.9 times higher than that at a mix ratio of SW:DFW = 1:0.5. These results showed that C. pyrenoidosa can be used to remove nutrients from mixed wastewater sources and simultaneously produce algal lipids.