Accumulating evidence indicates that elevated homocysteine (Hcy) level occurs in first-episode schizophrenia (FES) patients. We included 56 FES patients and 53 healthy controls (HC). Plasma level of Hcy was significantly higher in FES patients than HC ( p = 0.044). In addition, plasma levels of high-density lipoproteins (HDL) and folate were significantly lower in FES than in HC ( p < 0.001). Positive family history of schizophrenia was associated with lower plasma HDL ( p = 0.041) and vitamin B12 ( p = 0.017), as well as higher level of Hcy ( p = 0.017). Patients with FES, who abused cannabis, had higher levels of Hcy ( p = 0.017), as well as lower levels of vitamin B12 ( p = 0.017) and HDL ( p = 0.041). Plasma Hcy negatively correlated with duration of untreated psychosis ( r = −0.272, p = 0.042). There was a positive correlation between Hcy level and the severity of negative symptoms ( r = 0.363, p = 0.006) and general psychopathology ( r = 0.349, p = 0.008) assessed using Positive and Negative Syndrome Scale (PANSS). Vitamin B12 level was negatively associated with the severity of negative symptoms ( r = −0.406, p = 0.002), while folate level negatively correlated with general psychopathology score ( r = −0.365, p = 0.006) in PANSS. These results indicate that the severity of one-carbon metabolism alterations and HDL deficiency might be associated with family history of schizophrenia and cannabis abuse. Lower vitamin B12 and folate along with elevated Hcy may influence the severity of FES psychopathology.