The invention discloses STATCOM reference voltage determining and controlling methods of a transformer substation hydraulic reactive compensation system, wherein the STATCOM reference voltage determining method is based on an STATCOM first average reactive power duty ratio obtained based on a time window; furthermore whether the STATCOM first average reactive power duty ratio is large than or equal with a first ratio is satisfied is determined; and if yes, a change amount from the current control period to the next control period is calculated through a fuzzy logic controller and performing accumulation for calculating the STATCOM AC reference voltage of the next control period. According to the STATCOM reference voltage controlling method, a switching operation of a parallel capacitor FCand a reactor FL is controlled based on an STATCOM second average reactive power duty ratio which is obtained by the other time window. According to the STATCOM reference voltage determining and controlling methods, the magnitude of the high-voltage side reference voltage of the transformer substation in real time, thereby realizing purposes of controlling the reactive output of the STATCOM, adjusting the dynamic reactive standby capacity of the system, reducing the number of switching of FC and FL and prolonging service life of the FC and FL.