ADC采样频率,与定时器无关吧.你是用的定时器触发ADC采样吗?
ADC推荐使用DMA方式来进行.
给你一个初始化例程
void adcConfig(void)
{
        ADC_InitTypeDef ADC_InitStructure;
        DMA_InitTypeDef DMA_InitStructure;

        ADC_DeInit(ADC1);

        RCC_APB2PeriphClockCmd(RCC_APB2Periph_ADC1,ENABLE);

        RCC_AHBPeriphClockCmd(RCC_AHBPeriph_DMA1,ENABLE);

        DMA_DeInit(DMA1_Channel1);
        DMA_InitStructure.DMA_PeripheralBaseAddr = (uint32_t) &ADC1->DR;
        DMA_InitStructure.DMA_MemoryBaseAddr = (ui)adcbuf;
        DMA_InitStructure.DMA_DIR = DMA_DIR_PeripheralSRC;
        DMA_InitStructure.DMA_BufferSize = 8;                        //8级缓冲区,将来用来求取平均值
        DMA_InitStructure.DMA_PeripheralInc = DMA_PeripheralInc_Disable;
        DMA_InitStructure.DMA_MemoryInc = DMA_MemoryInc_Enable;
        DMA_InitStructure.DMA_PeripheralDataSize = DMA_PeripheralDataSize_HalfWord;
        DMA_InitStructure.DMA_MemoryDataSize = DMA_MemoryDataSize_HalfWord;
        DMA_InitStructure.DMA_Mode = DMA_Mode_Circular;
        DMA_InitStructure.DMA_Priority = DMA_Priority_High;
        DMA_InitStructure.DMA_M2M = DMA_M2M_Disable;
        DMA_Init(DMA1_Channel1,&DMA_InitStructure);

        DMA_Cmd(DMA1_Channel1,ENABLE);

        ADC_DMARequestModeConfig(ADC1,ADC_DMAMode_Circular);

        ADC_DMACmd(ADC1,ENABLE);

        ADC_StructInit(&ADC_InitStructure);


        ADC_InitStructure.ADC_Resolution = ADC_Resolution_12b; //12位精度
        ADC_InitStructure.ADC_ContinuousConvMode = ENABLE; //ADC连续转换模式
        ADC_InitStructure.ADC_ExternalTrigConvEdge = ADC_ExternalTrigConvEdge_None; //无外部触发模式
        ADC_InitStructure.ADC_DataAlign = ADC_DataAlign_Right; //右对齐方式
        ADC_InitStructure.ADC_ScanDirection = ADC_ScanDirection_Upward; //扫描方向
        ADC_Init(ADC1,&ADC_InitStructure);
        ADC_ChannelConfig(ADC1,ADC_Channel_5,ADC_SampleTime_71_5Cycles); // 精度影响结果.低精度的不可靠.
        ADC_GetCalibrationFactor(ADC1);
        ADC_Cmd(ADC1,ENABLE);

        while (!ADC_GetFlagStatus(ADC1,ADC_FLAG_ADEN));

        ADC_StartOfConversion(ADC1);
}

//ADC_SampleTime_71_5Cycles 这个参数不宜太小..否则,精度不够.